Bi-directionally cloned random cDNA expression vector libraries, compositions and methods of use

ABSTRACT

The present invention provides random cDNA expression vector libraries, comprising expression vectors which comprise random cDNAs positioned in sense and antisense orientation, which are useful for the delivery and expression of a combination of genetic effector types to host cells. Methods for producing these libraries through bi-directional cloning of random cDNAs are also provided. Also provided herein are methods of using these libraries to screen for agents capable of modulating cell phenotype in desirable ways.

FIELD OF THE INVENTION

The present invention relates generally to the field of molecular biology and in particular to the creation and use of gene libraries containing cloned cDNAs that encode expressed genes.

BACKGROUND OF THE INVENTION

A common practice in molecular biology is to create “gene libraries,” which are collections of cloned fragments of DNA that represent genetic information in an organism, tissue or cell type. To construct a library, desired DNA fragments are prepared and inserted by molecular techniques into self-replicating units generally called cloning vectors. Each DNA fragment is therefore represented as part of an individual molecule, which can be reproduced in a single bacterial colony or bacteriophage plaque. Individual clones of interest can be identified by various screening methods, and then grown and purified in large quantities to allow study of gene organization, structure and function.

Only a small fraction of the genetic information for an organism is actually used in an individual cell or tissue at a particular time. A cDNA library is a type of gene library in which only DNA for actively expressed genes is cloned. These active genes can be selectively cloned over silent genes because the DNA for active genes is transcribed into messenger RNA (mRNA) as part of the pathway by which proteins are made. RNA molecules are polar in nature, i.e. the constituent nucleoside bases are linked via phosphodiester bonds between the 3′ ribosyl position of one nucleoside and the 5′ ribosyl position on the following nucleoside. RNA is synthesized in the 5′ to 3′ direction, and mRNAs are read by ribosomes in the same direction, such that proteins are synthesized from N-terminus to C-terminus. Over the past decade, cDNA libraries have become the standard source from which thousands of genes have been isolated for further study.

cDNA libraries may be expression libraries, whereby the cDNAs are transcribed and translated, resulting in the production of polypeptides corresponding to mRNA-encoded proteins. The activity of cDNA expression products may be assayed, and the function of corresponding mRNAs and proteins encoded thereby may be determined.

Full length cDNA, which comprises the entire open reading frame (ORF) of an mRNA, is desirable for many applications. Alternatively, partial cDNA and cDNA fragments are useful in some applications, for example, identifying domains within proteins, and for identifying genetic effectors having desirable activity. Interestingly, microdomains can exert unique biological effects compared to the parental molecules from which they are derived (Lorens et. al., Mol. Therapy, 1:438-447, 2000). The ability to express protein microdomains can be a powerful means to subtly perturb cellular physiology in manners that reveal new paths for therapeutic intervention.

The use of retroviruses is desirable for the stable transduction of genetic material into host cells, particularly host cells which are poorly transfectable, such as myoblasts and lymphocytes.

One object of the present invention is to provide methods and compositions for stably expressing genetic effectors, comprising random cDNAs, in host cells.

An additional object of the invention is to provide methods and compositions to screen for genetic effectors, comprising random cDNAs, that alter cell phenotype in a desirable way.

SUMMARY OF THE INVENTION

The present invention provides methods and compositions for producing bi-directional random cDNA libraries. Bi-directional random cDNA libraries comprising pluralities of random cDNA expression vectors, which plurality is a mixture of vectors having cDNAs in sense and antisense orientation, are also provided. In a preferred embodiment, the random cDNA expression vectors provided herein comprise random cDNA fragments. Methods of using these libraries are also provided.

In one aspect of the invention, bi-directional random cDNA expression vector libraries are provided. Each library comprises a plurality of random cDNA expression vectors. Each library further comprises three different types of random cDNA expression vectors which differ in the orientation and translational frame of the cDNA inserts therein and in the expression products they produce. In the first vector type, a random cDNA is operably linked to transcriptional and translational regulatory sequences in sense orientation and in frame. In the second vector type, a random cDNA is operably linked to transcriptional and translational regulatory sequences in sense orientation and out of frame. In the third vector type, a random cDNA is operably linked to transcriptional regulatory sequence in antisense orientation.

Methods for synthesizing bi-directional random cDNA expression vector libraries comprising the three different types of vectors are also provided herein. An important, desirable feature of these methods is that separate synthesis steps are not required to produce these three different types of random cDNA expression vectors.

It will be understood that the cDNA libraries of the present invention comprise vectors, which comprise random cDNAs, which random cDNAs are positioned in expression vectors in sense or antisense orientation (bi-directional). These libraries are sometimes referred to herein as bi-directional random cDNA libraries. For the ease of description, the terms “bi-directional” and “random” will often be omitted when referring herein to these libraries and methods of making the same.

In a preferred embodiment, the expression vector library comprises a plurality of expression vectors, each vector comprising a) a first nucleic acid comprising a cDNA; b) a second nucleic acid which is a fusion partner, and c) a transcriptional regulatory sequence recognized by a host cell, wherein the first and second nucleic acids form a fusion nucleic acid which is operably linked to the transcriptional regulatory region (sometimes referred to herein as a transcriptional regulatory sequence). The vectors also comprise a translational regulatory region (sometimes referred to herein as a translational regulatory sequence) which forms part of the fusion nucleic acid and initiates translation of the fusion nucleic acid.

In a preferred embodiment, the cDNA is a cDNA restriction fragment, preferably between about 0.2 and about 2.0 kb in size.

In a preferred embodiment, the fusion partner encodes a detectable protein. In a preferred embodiment, the detectable protein is an autofluorescent protein. In a further preferred embodiment, the autofluorescent protein is a green fluorescent protein (GFP). In a further preferred embodiment, the autofluorescent protein is a GFP from Aequorea, or one of the well known variants thereof including red flourescent protein (RFP), blue fluorescent protein (BFP), and yellow fluorescent protein (YFP). In another further preferred embodiment, the autofluorescent protein is a GFP from Renilla. In another further preferred embodiment, the autofluorescent protein is a GFP from Ptilosarcus. In another preferred embodiment, the autofluorescent protein is a GFP homologue from Anthozoa species (Matz et al., Nat. Biotech., 17:969-973, 1999).

In a preferred embodiment, the first nucleic acid is fused to the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid wherein cDNA encoded sequence is located at the 3′ end and nucleic acid sequence encoding detectable protein is located at the 5′ end. Expression products also include a fusion protein that comprises a C-terminal polypeptide encoded by cDNA and an N-terminal polypeptide which is a detectable protein moiety. In a library comprising such, vectors, some cDNAs will translate in frame while others will translate out of frame, encoding what are herein referred to as “random peptides”. As cDNA is also inserted in antisense orientation, the expression products include fusion nucleic acids wherein antisense nucleic acid is located at the 3′ end and nucleic acid sequence encoding detectable protein is located at the 5′ end. The expression products also include fusion proteins that comprise C-terminal polypeptide encoded by an antisense cDNA transcript, also referred to herein as “random peptide”, and an N-terminal polypeptide which is a detectable protein moiety.

The libraries provided herein comprise mixtures of vectors having cDNAs in sense or antisense orientation. cDNAs in sense orientation in the expression vectors provided herein may be translated in frame or out of frame, as discussed further below. In addition, cDNAs in antsense orientation may also be translated. Accordingly, internal “stop” codons (TAA, TGA, TAG) may be encountered, interrupting or inhibiting translation. For clarity of description, the occurrence of internal translational “stop” codons within antisense cDNAs and cDNAs translated out of frame is not treated in every embodiment discussed herein, though it is understood that such “stop” codons may occur.

In another embodiment, the first nucleic acid is fused to the 5′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid wherein cDNA encoded sequence is located at the 5′ end and nucleic acid sequence encoding detectable protein is located at the 3′ end. Expression products also include a fusion protein that comprises an N-terminal. polypeptide encoded by cDNA and a C-terminal polypeptide which is a detectable protein moiety. In libraries comprising such vectors, some cDNAs will translate in frame while others will translate out of frame as random peptides. As cDNA is also inserted in antisense orientation, the expression products include fusion nucleic acids wherein antsense nucleic acid is located at the 5′ end and nucleic acid sequence encoding detectable protein is located at the 3′ end. The expression products also include fusion proteins that comprise N-terminal polypeptide encoded by an antsense cDNA transcript (random peptide) and a C-terminal polypeptide which is a detectable protein moiety.

In another embodiment, the first nucleic acid is positioned within the second nucleic acid (e.g., the second nucleic acid comprises the first nucleic acid). Expression products of such vectors include fusion nucleic acids wherein cDNA-encoded sequence is located within nucleic acid sequence encoding detectable protein. Expression products also include fusion proteins that comprise cDNA-encoded peptides within detectable proteins, preferably in the surface exposed loop region of a detectable protein, as described herein. In libraries comprising such vectors, some cDNAs will translate in frame while others will translate out of frame as random peptides. As cDNA is also inserted in antisense orientation, the expression products include fusion nucleic acids wherein antisense nucleic acid is located within nucleic acid sequence encoding detectable protein. The expression products also include fusion proteins that comprise antisense cDNA-encoded peptides (random peptides) within detectable proteins.

In a preferred embodiment, the expression vector additionally comprises a third nucleic acid sequence, referred to herein as a linker, which is interposed between the first and second nucleic acids. In this embodiment, the linker may encode a linking peptide that joins cDNA encoded peptide to the detectable protein moiety in a fusion protein. Alternatively, the linker may be a separation sequence that provides for the expression of separate cDNA encoded peptide and detectable protein moieties.

In a preferred embodiment, the linker encodes a peptide linker that joins cDNA encoded peptide to the detectable protein moiety in a fusion protein. Such a linker may be used to fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. Preferably, cDNA-encoded peptide is C-terminal to the detectable protein moiety in the fusion protein. Preferably, the detectable protein is GFP. Preferred linkers are rich in the amino acids glycine and serine, as described herein, and are from about 20 to about 30, more preferably about 25 to about 28 amino acids in length.

In one embodiment, the linker connecting the first and second nucleic acids comprises an internal ribosome entry site (IRES). Such a linker may be used to fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid and two separate polypeptides translated from a fusion nucleic acid, particularly a first polypeptide which is encoded by a cDNA, and a second polypeptide which is a detectable protein.

In one embodiment, the linker connecting the first and second nucleic acids comprises a cleavage site. Such a linker may fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid, and a fusion protein wherein the cDNA-encoded polypeptide moiety and the detectable protein moiety are separated by an intervening cleavage site which is a polypeptide sequence that is recognized by a protease. This site provides for cleavage of the covalent peptide linkage which fuses the cDNA-encoded polypeptide moiety to the detectable protein moiety in the fusion protein and thereby provides for the expression of two separate polypeptides.

In one embodiment, the linker is a separation sequence comprising a 2a sequence, as described below. Such a linker may fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid and two separate polypeptides translated from a fusion nucleic acid, particularly a first polypeptide which is encoded by a cDNA, and a second polypeptide which is a detectable protein.

In a preferred embodiment, the cDNA expression vectors comprise a fusion partner in addition to the second nucleic acid encoding a detectable protein. The fusion partner may be fused or linked to the first or second nucleic acid, or both.

In some embodiments, the second nucleic acid is a fusion partner other than a fusion partner encoding a detectable protein.

In one aspect of the invention, methods for synthesizing cDNA expression vector libraries comprising the three different types of vectors described above (i.e. cDNA in sense orientation and in frame; in sense orientation and out of frame; and in antisense orientation) are provided. The methods involve the use of adaptors to bidirectionally clone random cDNAs, preferably random cDNA restriction fragments of between about 0.2 to about 2.0 kb.

In an especially preferred embodiment, the cDNA expression vectors provided are retroviral vectors. Accordingly, retroviral cDNA expression vectors and libraries comprising the same are provided herein. Each library comprises three different types of cDNA expression vectors which differ in the orientation and translational frame of the cDNA inserts therein and in the expression products they produce. In the first vector type, a random cDNA is operably linked to transcriptional and translational regulatory sequences in sense orientation and in frame. In the second vector type, a random cDNA is operably linked to transcriptional and translational regulatory sequences in sense orientation and out of frame. In the third vector type, a random cDNA is operably linked to transcriptional regulatory sequence in antisense orientation.

In a preferred embodiment, the retroviral cDNA expression vectors provided herein comprise a self-inactivating 3′ long terminal repeat (LTR) region which is located 3′ of the first and second nucleic acids. These vectors are sometimes referred to as SIN vectors.

In a preferred embodiment, the retroviral cDNA expression vectors provided herein comprise a tetracycline-inducible (tet-inducible) promoter with an orientation opposite to the LTR and are SIN vectors. Preferred tetandudble promoters comprise multiple copies of the tet operon operably linked to a minimal human cytomegalovirus (CMV) promoter (for example, see Gossen et al., PNAS 89:5547-5551, 1992).

In one aspect of the invention, methods for synthesizing retroviral cDNA expression vector libraries comprising the three different types of vectors described above (i.e. cDNA in sense orientation and in frame; in sense orientation and out of frame; and in antisense orientation) are provided. The methods involve the use of adaptors to bidirectionally clone random cDNAs, preferably random cDNA restriction fragments of between about 0.2 to about 2.0 kb.

In one aspect of the invention, methods of screening for a bioactive agent capable of altering the phenotype of a cell in a desirable way are provided. In one embodiment, the method comprises the steps of a) introducing a cDNA expression vector library into a plurality of cells; b) screening the plurality of cells for a cell exhibiting a phenotype which is altered in a desirable way, wherein the altered phenotype is due to the expression of a cDNA. The method may also comprise any of the steps of c) isolating at least one cell exhibiting an altered phenotype; d) isolating a nucleic acid comprising the cDNA from the cell exhibiting an altered phenotype; e) identifying the bioactive agent; and f) identifying and/or isolating the molecule(s) to which the agent binds. Additionally, in some preferred embodiments, the methods involve stimulating the plurality of cells in manner known to produce a disease-like behavioral response or a phenotype of the disease process. In an especially preferred embodiment, retroviral cDNA libraries provided herein are used.

In another embodiment, the method comprises the steps of a) introducing a cDNA expression vector library into a first plurality of cells; b) contacting the first plurality of cells with a second plurality of cells; and c) screening the second plurality of cells for a cell exhibiting a phenotype which is altered in a desirable way, wherein the altered phenotype is due to contact with the first plurality of cells and expression of cDNA in the first plurality of cells. The method may also comprise any of the steps of d) isolating a cell from the first plurality of cells which is contacted with at least one cell in the second plurality of cells exhibiting an altered phenotype; e) isolating a nucleic acid comprising the cDNA from the cell isolated from the first plurality of cells; f) identifying the bioactive agent; and g) identifying and/or isolating the molecule(s) to which the agent binds. In an especially preferred embodiment, retroviral cDNA libraries provided herein are used.

In preferred embodiments, methods of screening for bioactive agents capable of modulating the following physiological processes or biochemical activities are provided: IgE production in B cells; mast cell activation by IgE binding; mast cell degranulation; B cell activation and antibody secretion in response to antigen receptor stimulation; T cell activation in response to antigen receptor stimulation; epithelial cell activation; E3 ubiquitin ligase activity; inflammation induced by E3 ubiquitin ligase activity; inflammation induced by TNF activity; apoptosis in activated T cells; angiogenesis; uncontrolled cell proliferation; uncontrolled cell proliferation mediated by E3 ubiquitin ligase activity; and translation of Hepatitis C-encoded proteins.

Bioactive agents interact with target molecules to modulate cell phenotype. Provided herein are methods for isolating and. identifying a target molecule using either the cDNA insert of a retroviral cDNA expression vector or an expression product thereof, including nucleic acids and polypeptides. Target molecules may be used to characterize signaling pathways, provide lead compounds for pharmaceutical development, and to screen for bioactive agents, including small molecule chemical compounds, capable of modulating target molecule activity.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic diagram showing a GFP C-terminal fusion library retroviral vector. cDNA is inserted 3′ of GFP-encoding nucleic acid, and a linker is interposed between the two. The resultant fusion protein comprises N-terminal GFP fused to cDNA-encoded peptide through a linker peptide. A triple frame stop cassette is situated 3′ of the cDNA to ensure translation is stopped. In addition, the vector comprises a retroviral packing sequence (ψ), and a primer landing pad sequence, which provides for efficient PCR priming. cDNA is inserted between 2 BstXI sites in the vector using adaptors described herein.

FIG. 2 describes the products of the bidirectional cDNA cloning strategy, where cDNA is fused to the 3′ terminus of GFP-encoding nucleic acid. cDNA may be inserted in sense orientation in frame or out of frame. Expression products include GFP fused to cDNA-encoded protein which is in frame or out of frame (peptide). cDNA may also be inserted in antisense orientation, and expression products are antisense nucleic acid, and translated GFP-antsense cDNA-encoded (peptide) fusion protein.

FIG. 3 is a schematic diagram showing two of the preferred retroviral expression vectors for use in the generation of GFP C-terminal cDNA fusion libraries.

The vector pG3-Z comprises a composite CRU5 promoter which drives expression of the Renilla GFP fusion construct. cDNA is inserted 3′ of GFP-encoding nucleic acid using a multiple cloning site which comprises two BstXI sites. cDNA may be inserted into these sites with the use of adaptors. Downstream of the cDNA insert site is a triple frame translation STOP cassette, which ensures translation of the GFP-cDNA fusion protein is stopped appropriately. In addition the pG3-Z vector comprises a retroviral packaging sequence (ψ), and a primer landing pad sequence, which provides for efficient PCR priming.

The vector pTRA-G3-Z comprises a tet-inducible promoter, which comprises a minimal human CMV promoter and seven tet inducible operons arranged in tandem. The tet-inducible promoter drives expression of the downstream GFP fusion construct. The tet-inducible promoter has an orientation opposite to that of the LTR. The vector is a SIN vector, in which the 3′LTR is mutated within enhancer elements. cDNA is inserted 3′ of GFP-encoding nucleic acid using a multiple cloning site which comprises two BstXI sites. cDNA may be inserted into these sites with the use of adaptors. Downstream of the cDNA insert site is a triple frame translation STOP cassette, which ensures translation of the GFP-cDNA fusion protein is stopped appropriately. In addition the pG3-Z vector comprises a retroviral packaging sequence (ψ), and a primer landing pad sequence, which provides for efficient PCR priming.

FIG. 4 is a schematic diagram which depicts the cloning method used to generate GFP C-terminal cDNA fusions. cDNA is synthesized by poly-dT and/or random hexamer (N6) primed reverse transcriptase reactions. Second strand cDNA is produced by a standard DNA polymerase I reaction. cDNA is then cleaved with different restriction enzymes to produce various sized fragments. The cDNA is then size-selected and ligated to BstXl adaptors. These adaptors generate a Notl cleavage site when ligated as a dimer. The adaptor-modified cDNA pool is then cut with NotI to remove adaptor dimers, and purified adaptor-modified cDNA is then cloned into BstxI cut vector DNA and propagated in E. coli.

FIG. 5 shows the sequence of the multiple cloning site of the preferred retroviral expression vectors shown in FIG. 4, following insertion of adaptor-modified cDNA. The sequence of preferred adaptors is also shown. The C-terminal amino acid sequence of the GFP moiety is shown with the encoded linker amino acids and the encoded adaptor sequence. Downstream of the cDNA is the three-frame stop codon cassette. Two different BstXI adaptor sequences are displayed.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods and compositions for producing bi-directional random cDNA libraries. Bi-directional random cDNA libraries comprising pluralities of random cDNA expression vectors, which pluralities are each mixtures of vectors having cDNAs in sense and antisense orientation, are also provided. In a preferred embodiment, the random cDNA expression vectors provided herein comprise random cDNA fragments. Methods of using these libraries are also provided.

In a preferred embodiment, the cDNA expression vector libraries provided herein each comprise three different types of cDNA expression vectors which differ in the orientation and translational frame of the cDNA inserts therein and in the expression products they produce. Each vector comprises a cDNA which is operably linked to transcriptional and translational regulatory sequences in one of three ways; in sense orientation and in frame; in sense orientation and out of frame; and in antsense orientation.

cDNA encoded transcripts produced by the present expression vectors may be translated in frame or out of frame, as discussed herein. In addition, cDNA encoded antisense transcripts may be translated. Accordingly, internal “stop” codons (TAA, TGA, TAG) may be encountered, interrupting or inhibiting translation. For clarity of description, the occurrence of internal translational “stop” codons in antisense transcripts and transcripts having open reading frames (ORFs) that are out of frame with respect to native ORFs is not treated in every embodiment discussed herein, though it is understood that such “stop” codons may occur.

As used herein, the term “cDNA” means DNA that corresponds to or is complementary to at least a portion of messenger RNA (mRNA) sequence and is generally synthesized from an mRNA preparation using reverse transcriptase or other methods. cDNA as used herein includes full length cDNA, corresponding to or complementary in sequence to full length mRNA sequences, partial cDNA, corresponding to or complementary in sequence to portions of mRNA sequences, and cDNA fragments, also corresponding to or complementary to portions of mRNA sequences. It should be understood that references to a particular “number” of cDNAs or other nucleic acids actually refers to the number of clones, cDNA sequences or species, rather than the number of physical copies of substantially identical sequences present. Moreover, the term is often used to refer to cDNA sequences incorporated into a plasmid or viral vector which can, in turn, be present in a bacterial cell, mammalian packaging cell line, or host cell.

By “cDNA fragment” is meant a portion of a cDNA that is derived by fragmentation of a larger cDNA. cDNA fragments may be derived from partial or full length cDNAs. As will be appreciated, a number of methods may be used to generate cDNA fragments. For example, cDNA may be subjected to shearing forces in solution that can break the covalent bonds of the backbone of the cDNA. In a preferred embodiment, cDNA fragments are generated by digesting cDNA with restriction endonuclease(s). Other methods are well known in the art.

“Partial cDNA” refers to cDNA that comprises part of the nucleic acid sequence which corresponds to or is complementary to the open reading frame (ORF) of the corresponding mRNA.

“Full length cDNA” refers to cDNA that comprises the complete sequence which is complementary to or corresponds to the ORF of the corresponding mRNA. In some instances, which are clear, full length cDNA refers to cDNA that comprises sequence complementary to or corresponding to the 5′ untranslated region (UTR) of the corresponding mRNA, in addition to sequence which is complementary to or corresponds to the complete ORF.

A corresponding mRNA comprises the nucleotide sequence of the mRNA used as template for synthesis of a particular cDNA, or is the template mRNA used for synthesis of a particular cDNA.

The occurrence of alternatively spliced mRNAs in an mRNA pool used to make cDNA may lead to the synthesis of a cDNA which has sequence corresponding to more than one mRNA type. In addition, the cDNA may comprise a nucleotide sequence that is identical to only a segment of an alternatively spliced mRNA.

By “libraries” is meant a plurality. In a preferred embodiment, the cDNA expression vector libraries provided herein comprise between about 10³ and about 10⁹ independent clones, with from about 10⁵ to about 10⁸ being preferred, and about 10⁵ to about 10⁶ being especially preferred.

In one aspect, provided herein are methods for producing bi-directionally cloned, random cDNA expression vector libraries. The methods involve the use of adaptors to clone random cDNAs into expression vectors bi-directionally. In a preferred embodiment, the cDNAs used are cDNA fragments, preferably restriction fragments. In a preferred embodiment, methods for producing retroviral cDNA expression vector libraries are provided.

It will be appreciated that the present methods, involving digestion of cDNA with restriction endonucleases, and modification of cDNA restriction fragments with adaptors that provide for bi-directional cloning into expression vectors, provide for the synthesis of the three types of vectors described above in a single process, which is desirable.

Bi-directional, or non-directional cloning, involves the insertion of cDNA in either of the two possible orientations, whereby half of the cDNA is inserted in sense orientation and half of the cDNA is inserted in antisense orientation. Non-directional cloning can be achieved through the use of identical adaptor-modified cDNA ends and complementary vector cloning site sequences.

General methods for producing cDNA libraries are known in the art (Blumberg et al. Science 253:194-196 (1991); Cho et al. Cell 67:1111-1120 (1991); Hawley et al. Genes Dev. 9:2923-2935 (1995)).

Methods for constructing cDNA libraries from mRNA isolated from a cellular source are well known in the art. General protocols are, for example, disclosed in Current Protocols in Molecular Biology, John Wiley & Sons, Ausubel et. al. eds., 1988, updated October 2001, Chapter 5, Construction of Recombinant DNA Libraries, particularly Section III, Preparation of Insert DNA from Messenger RNA, expressly incorporated herein by reference. Additionally, two commonly used methods of producing cDNA from mRNA are described in Okayama and Berg, Mol. Cell Biol. 2, 161-170 (1982) and Gubler and Hoffman, Gene 25 263-269, (1983).

In a typical procedure, poly(A)+ mRNAs are isolated from cells. However, isolated RNA that is not poly(A)+ enriched may also be used.

Methods for isolating RNA from eukafyotic and prokaryotc cells are well known in the art. For example, see Current Protocols in Molecular Biology, John Wiley & Sons, Ausubel et. al. eds., 1988, updated October 2001, Chapter 4, Preparation of RNA from Eukaryotic and Prokaryotic Cells, expressly incorporated herein by reference; Molecular Cloning: A Laboratory Manual, 3^(rd) Edition, Sambrook et al. eds., Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 2001, ISBN 0-87969-577-3. Poly(A)+, which is greatly enriched in mRNA can be separated from the remainder of total RNA, which is largely ribosomal RNA (rRNA) and transfer RNA (tRNA), for example, by binding to oligo(dT) cellulose (e.g., latex beads) while the remainder washes through. The poly(A)+ mRNA can be eluted from the beads following known procedures, such as the protocol described in Ausubel et al., supra, Unit 4.5. Some other protocols use poly(U)Sephadex instead of oligo(dT). See, e.g. Moore and Sharp, Cell 36, 581-591 (1984). A preferred method is that of Chomczynski and Sacchi, Anal. Biochem. 162:156-159 (1987). The RNA can be from any organism.

The initial mRNA may be present in a variety of different samples, where the sample will typically be derived from a physiological source. The physiological source may be derived from a variety of eukaryotic and prokaryotic sources. In addition, viral RNA may be used to serve as template for cDNA synthesis. Physiological sources of interest including sources derived from single celled organisms such as yeast and multicellular organisms, including plants and animals, particularly mammals, preferably humans, primates and rodents, where the physiological sources from multicellular organisms may be derived from particular organs or tissues of the multicellular organism, or from isolated cells derived therefrom. In obtaining the sample of RNAs from the physiological source from which it is derived, the physiological source may be subjected to a number of different processing steps, where such processing steps might include tissue homogenization, cell isolation and cytoplasmic extraction, nucleic acid extraction and the like, where such processing steps are known to the those of skill in the art. Eukaryotic and prokaryotic sources include, but are not limited to, bacteria, plant, fungi, insect and mammalian sources, which include, but are not limited to, algae, Arabidopsis thaliana, Aspergillus, Axolotl, baboon, bovine, barley, canine, carp, chicken, corn, Drosophila melanogaster, feline, firefly, frog, Fugu fish, hamster, human, lobster, monkey, mouse, nematode, opposum, pea, porcine, rabbit, rat, rice, sea urchin, sheep, soybean, spinach, tobacco, tomato, wheat, Xenopus laevis, yeast, and zebrafish. Preferred sources of RNA for use in the present invention are human, rodent, and primate. Tissue and cell sources for RNA include, but are not limited to, adipose, adrenal, adult brain, adult liver, adult ovary, amygdala, aorta, B-cell, T-cell, mast cell, bladder, blood, bone marrow, brain tumor, breast, breast tumor, capillary endothelial cells, carcinoma, cerebellum, cervix, chondrocyte, colon, colon tumor, colorectal adenocarcinoma, embryo, embryonic brain, embryonic adrenal, embryonic eye, embryonic gut, embryonic liver, embryonic lung, embryonic muscle, embryonic spleen, endothelial, epidermis, epithelial cell, erythroleukemia, esophageal tumor, esophagus, eye, fetus, fetal brain, fetal adrenal, fetal eye, fetal gut, fetal liver, fetal lung, fetal muscle, fetal spleen, fibroblast, fibrosarcoma, glioblastoma, glioma, heart, adult heart, HeLa, hepatocarcinoma, hepatoma, hippocampus, hypothalamus, intestine, small intestine, keratinocyte, kidney, kidney tumor, liver, liver tumor, lung, lung tumor, lymph node, lymphocyte, lymphoblast, lymphoma, macrophage, microglia, mammary gland, mucus-producing gland, muscle, myoblast, monocyte, nasal mucosa, neuronal, NIH 3T3, stomach, thyroid, uterus, oocyte, pancreas, ovarian tumor, pituitary, prostate, rectal tumor, rectum, retina, salivary gland, spinal cord, spleen, submucosa, stem cell, and tonsil. Viral nucleic acids may also be used.

Once isolated, mRNAs are then used as template for the synthesis of double stranded cDNA (dscDNA) using the enzyme reverse transcriptase. Synthesis of cDNA may be done in vitro or in vivo, as is known (for example, see U.S. Pat. No. 5,891,637, issued 6 Apr. 1999 to Ruppert et. al, incorporated herein be reference).

Reverse transcriptases have been traditionally purified from retroviruses, such as avian myoblastosis virus (AMV) and Moloney murine leukemia virus (M-MuLV), which use them to make DNA copies of their own RNA genomes. The M-MuLV reverse transcriptase has also been purified from overproducing E. coli cells containing the cloned gene. Tanese et al. in PNAS USA 82, 4944-4948 (1985) and Roth et al. in J. Biol. Chem. 260(16), 9326-9335 (1985) report on the expression, isolation and characterization of a reverse transcriptase isolated from Moloney murine leukemia virus (M-MuLV). This reverse transcriptase is encoded by the viral pol gene and is a monomer having a molecular weight of about 80 kD. See also U.S. Pat. No. 4,943,531.

In the process of converting mRNA into double stranded cDNA in vitro, a first cDNA strand is synthesized by the reverse transcriptase. A DNA polymerase, such as E. coli DNA polymerase, then uses the first cDNA strand as a template for the synthesis of the second cDNA strand, thereby producing a population of dscDNA molecules from the original poly(A)+ mRNA. In a preferred embodiment, the dscDNA is cleaved with one or more restriction endonucleases, ligated to adaptors, and adaptor-modified cDNA fragments of preferably between about 0.2 and about 2.0 kb are bi-directionally cloned into expression vectors.

First strand cDNA synthesis is performed using any convenient protocol. In preparing the first strand cDNA, a primer is contacted with the mRNA, a reverse transcriptase, and other reagents necessary for primer extension under conditions sufficient for first strand cDNA synthesis to occur. Both random and specific primers may be employed, including specific oligo dT primers that provide for hybridization to the polyA tail of an mRNA. Oligo dT primers provide for the synthesis of full length cDNAs. The oligo dT primer will be sufficiently long to provide for efficient hybridization to the polyA tail, where the primer will typically range in length from 10 to 25 nucleotides (nt) in length, usually 10 to 20 nt in length, and more usually from 12 to 18 nt length.

In a preferred embodiment, random primers are used for cDNA synthesis. Preferred random primers are about 6 nucleotides in length, denoted N₆.

By random primers is meant random sequence primers, in which each of the nucleotide positions is occupied by a nucleotide selected at random from among a complete set of possibilities, but commonly limited to the four nucleotides, dAMP, dCMP, dGMP, or dTMP.

The use of random primers is well known in the art. For example, see Sambrook et al., supra.

As will be appreciated, when random primers are used, non-poly(A)+ RNA may also be reverse transcribed. Accordingly, in this embodiment, care is taken to ensure the RNA sample used is enriched in poly(A)+ RNA. Random primers typically provide for the synthesis of partial cDNAs.

Additional reagents that may be present include: dNTPs; buffering agents, e.g. TrisCI; cationic sources, both monovalent and divalent, e.g. KCl, MgCl₂; sulfhydril reagents, e.g. dithiothreitol; and the like. A variety of enzymes, usually DNA polymerases, possessing reverse transcriptase activity can be used for the first strand cDNA synthesis step. Examples of suitable DNA polymerases are described above. Preferably, the DNA polymerase will be selected from the group consisting of Moloney murine leukemia virus (M-MLV) as described in U.S. Pat. No: 4,943,531 and M-MLV reverse transcriptase lacking RNaseH activity as described in U.S. Pat. No. 5,405,776 (the disclosures of which patents are herein incorporated by reference), human T-cell leukemia virus type I (HTLV-I), bovine leukemia virus (BLV), Rous sarcoma virus (RSV), human immunodeficiency virus (HIV) and Thermus aquaticus (Taq) or Thermus thermophilus (Tth) as described in U.S. Pat. No. 5,322,770, the disclosure of which is herein incorporated by reference, avian reverse transcriptase, and the like. Suitable DNA polymerases possessing reverse transcriptase activity may be isolated from an organism, obtained commercially or obtained from cells which express high levels of cloned genes encoding the polymerases by methods known to those of skill in the art, where the particular manner of obtaining the polymerase will be chosen based primarily on factors such as convenience, cost, availability and the like. Of particular interest because of their commercial availability and well characterized properties are avian reverse transcriptase and M-MLV.

The order in which the reagents are combined may be modified as desired. One protocol that may be used is as follows.

The set of primers, random or poly dT, are mixed with the total RNA or poly(A)+ RNA and processed under suitable conditions to promote first strand cDNA synthesis. Initially, the mixture of primers and RNA is, for a sufficient time, brought to a temperature sufficiently high to denature double-stranded portions of the nucleic acids. A denaturing step at 70° C. for 10 minutes is generally suitable. While reaction components are added, the mixture is kept chilled to prevent renaturation or priming. Reaction components are added to bring the mixture to a suitable buffered pH and ionic strength, to allow RNA-dependent DNA synthesis to proceed. Also added to the reaction. are deoxynucleotide triphosphates for incorporation into the first cDNA strand and an RNA-dependent DNA polymerase as described above. A preferred reverse transcriptase is the Moloney murine leukemia virus reverse transcriptase.

When the first strand synthesis reaction components have been added, the mixture is incubated for a sufficient time and at a temperature appropriate for RNA-dependent DNA polymerization. Incubation at 37° C. for 60 minutes is generally suitable. When first strand synthesis is complete, the reaction is heated to a sufficiently high temperature for an adequate length of time to inactivate the RNA-dependent DNA polymerase (e.g., 70° C. for 10 minutes).

In a preferred method, following first strand cDNA synthesis, the resultant duplex mRNA/cDNA (i.e. hybrid) is contacted with an RNAse capable of degrading single stranded RNA but not RNA complexed to DNA, under conditions sufficient for any single stranded RNA to be degraded. A variety of different RNAses may be employed, where known suitable RNAses include: RNAse Ti from Aspergillus orzyae, RNase I, RNase A and the like. The exact conditions and duration of incubation during this step will vary depending on the specific nuclease employed. However, the temperature is generally between about 20 to 37° C., and usually between about 25 to 37° C. Incubation usually lasts for a period of time ranging from about 10 to 60 min, usually from about 15 to 60 min.

Nuclease treatment results in the production of blunt-ended mRNA/cDNA duplexes or hybrids. In the resultant mixture, those mRNA/cDNA hybrids that include a full length cDNA will have the 5′ cap structure of the template mRNA.

For both randomly primed and poly T primed cDNA synthesis, second strand cDNA synthesis can proceed in the same reaction vessel as the first strand synthesis reaction. The reaction mixture is adjusted to buffering conditions appropriate for DNA polymerization using a DNA-dependent DNA polymerase. Also added to the second strand synthesis reaction are nucleotides for incorporation into a nascent second strand. Finally, an agent for introducing nicks into the RNA strand is added to the second strand reaction. By introducing nicks into the RNA strand, the DNA-dependent DNA polymerase can utilize the nicked RNA strands as primers for second strand DNA synthesis. During second strand synthesis, remaining RNA residues are displaced from the first strand by the growing second strand. A suitable nicking agent is RNase H (Okayama, H. and Berg, P. (1982) Mol. Cell. Biol. 2, 161; Gubler, U. and Hoffman, B. (1983) Gene 25, 263). When the reaction components have been added, the second strand synthesis reaction is allowed to proceed for a suitable length of time at a temperature adequate to support DNA-dependent DNA polymerization. A generally suitable incubation condition is 15° C. for 90 minutes. When second strand synthesis is complete, the double-stranded cDNA molecules thus formed are purified from the reaction components. Proteins can be inactivated and removed from the mixture by phenol:chloroform:isoamyl alcohol extraction. The double stranded cDNA is then precipitated with alcohol, centrifuged, and resuspended in water.

Alternatively, the first cDNA strand may be separated from mRNA using methods known in the art, and oligonucleotide primers may be used to prime synthesis of the second cDNA strand.

If desired, dCTP can be replaced in the reaction mix with 5-methyl dCTP. Incorporation of 5-methyl dCTP into the growing first strand protects the synthetic DNA from cleavage by restriction endonucleases. It is desirable in some applications to avoid internal cleavage of cDNAs formed by the method. dCTP can, if desired, be replaced with 5-methyl dCTP during synthesis of the second cDNA strand as well so that the second strand will also be methylated, and thereby protected from cleavage by restriction endonucleases. Hemi-methylated and fully-methylated DNA are protected from-cleavage by most restriction endonucleases.

Another acceptable method for protecting against digestion at internal sequences is to treat the cDNA fragments with a specific DNA methylase prior to adaptor ligation. In. one embodiment, cDNA is digested with restriction endonucleases and then methylated to prevent further digestion of the cDNA fragments later in the cloning procedure, for example, during digestion of adaptors, as described below.

However, in a preferred embodiment of the present methods, dCTP is not replaced with 5-methyl-dCTP during synthesis and cDNA is not treated with methylase, as digestion of the cDNA by restriction endonucleases to form cDNA fragments is desired.

Secondary structure in mRNA, which can decrease the efficiency of the synthesis of cDNA, can be reduced with the use of methylmercury hydroxide to destroy base pairing as is known in the art. However, cDNA yields are reduced with the use thereof (see Krug and Berger, Methods Enzymol., 152:313-325, 1987, incorporated herein by reference.

As is known, by altering the ratio of primers to mRNA in the synthesis of cDNA, the average. insert size (cDNA length) is modified. Decreasing the ratio of primer to mRNA increases the average cDNA length, while increasing the ratio of primer to mRNA decreases the average cDNA length. For some applications, shorter cDNA length may be desirable, for example, screening for functional domains of proteins, or screening for protein fragments with dominant negative activity. Additionally, shorter cDNA may be desired when cDNA is fused to a fusion partner that better accommodates smaller cDNA as opposed to longer cDNA, as described below. For other applications, longer cDNA sequences may be desired.

Following second strand. synthesis, 3′ single stranded protrusions or overhangs commonly remain on the cDNA due to dissociation of short primers near the termini. Therefore, it is desirable to remove any overhanging bases in the cDNA molecules thus formed. An appropriate enzyme for “trimming” 3′ extensions and/or adding terminal nucleotides to fill in 5′ overhang ends is T4 DNA polymerase.

Conditions for using T4 DNA polymerase to make double stranded DNA blunt ended are well known. For example, see Sambrook et al., supra.

Alternatively, in a preferred embodiment, following second strand synthesis, dscDNA is cleaved with selected restriction endonucleases to generate restriction fragments. These restriction fragments are then blunted with T4 DNA polymerase and used in place of uncut blunted dscDNA. In this way, cDNA fragments are produced.

The next step in the method is to ligate the cDNA molecule to a pair of adaptors, generating adaptor-modified cDNA. Adaptors may be ligated to cDNA using T4 DNA ligase. The same adaptors are ligated to both the 5′ and 3′ end of the cDNA. This provides the same adaptor overhang on each side of the cDNA molecule, facilitating bi-directional cloning of adaptor-modified cDNA, as described below.

cDNA is size-selected, with cDNAs of between about 0.2 and about 2.0 kb being preferred for use in the present methods of cDNA expression vector synthesis.

The adaptors used in the present methods have several features.

The initial adaptor sequence beginning at the 5′ terminus preferably forms one half of a symmetrical recognition sequence for a restriction endonuclease. This allows undesired adaptor dimers ligated at their blunt ends to be removed by digestion. When adaptors are ligated together as dimers, they may be cleaved with the appropriate restriction enzyme which recognizes the two restriction half sites fused together.

In addition, the adaptors comprise overhangs which are identical but not self complementary. Accordingly, preferred adaptors will not self ligate, other than blunt end to blunt end, and will leave free overhangs on adaptor-modified cDNA.

In a preferred embodiment, the adaptors encode a peptide linker used to link cDNA to a detectable protein moiety, preferably GFP, as described herein. Accordingly, the adaptors are designed so as not to introduce stop codons into the vector following ligation. Additionally, the adaptors are designed so as not to introduce disruptive amino acids, such as proline, or bulky amino acids, such as tryptophan, into the linker region. Amino acids with small side chains, such as serine, valine, glycine, are especially preferred, as further discussed below. Further, where the linker forms part of the N-terminus of a protein, before or following separation, or forms part of the N-terminus of a fusion protein, amino acids having hydrophobic side chains are typically avoided so as not to introduce an unwanted targeting or secretion signal. Conversely, in some embodiments described herein, a fusion partner which is a hydrophobic targeting sequence is desired and used.

Finally, the adaptors preferably provide for the excision of cDNA from expression vector. That is, the adaptors are designed such that cloning of adaptor-modified cDNA into vector preserves or generates useful restriction sites for cDNA excision.

Preferred adaptors for use in the present invention are described by the general sequence: 5′-p-C C G C N₁ N₂ N₃ N₄ N₅ C C A N₆ N₇ N₈ N₉ N₁₀   3′-G G C G N′₁ N′₂ N′₃ N′₄ N′₅ G G T N′₆-p-5′ wherein N₁ through N₁₀ are each any nucleotide, preferably a nucleotide selected from the group consisting of dAMP, dTMP, dGMP, dCMP, or analogs thereof which are known in the art, and wherein N′ denotes a nucleotide which is complementary to N.

As discussed above, in a preferred embodiment, the adaptor encodes part of a linker peptide sequence in a fusion protein. Accordingly, care is taken in the design of adaptors so as not to introduce a stop codon when cloning adaptor-modified cDNA into expression vector. Further, adaptor nucleotide sequence is selected to avoid introducing hydrophobic signals to the N-terminus, and to avoid introducing disruptive amino acids, such as proline, and bulky amino adds, such as tryptophan, into the linker region.

Nucleotides N₇ N₈ N₉ N₁₀ form a 3′ overhang which is not self-complementary, and thus identical free 3′ overhangs are generated at each end (opposite strands) of the dscDNA molecule. These overhangs are designed to be complementary to overhangs generated in the expression vector following digestion of the vector with BstXI. Further, cloning of the adaptor-modified cDNA into BstXI-cut vector generates flanking BstXI sites which may be used to excise the cDNA as desired.

Importantly, the use of identical adaptors-at each end of the cDNA provides for bidirectional cloning. Accordingly, about half of the adaptor-modified cDNAs are inserted in sense orientation, and about half are inserted in antisense orientation.

In addition, the 5′ terminus sequence of the adaptor, particularly C C G C, forms half of a Notl restriction enzyme recognition sequence (i.e. GCGGCCGC). Accordingly, adaptor dimers formed by blunt end ligation possess a Notl site, and unwanted adaptor dimers can conveniently be eliminated using the restriction endonuclease “NotI”.

Especially preferred adaptors for use in the present methods have the following nucleotide sequence: 5′-p-CCGCAGAACCCAGCACA-3′   3′-GGCGTCTTGGGTC-5′ or 5′-p-CCGCAGACTCCAGCACA-3′   3′-GGCGTCTGAGGTC-p-5′

Excess adaptors, and cut adaptor dimers, may be removed in a gel filtration step. cDNA is also size selected, with cDNAs between about 0.2 and about 2.0 kb being preferred.

Expression vectors for use with the preferred adaptors comprise two BstXI sites for bi-directional cloning of adaptor-modified random cDNAs. The BstXI sites are located in the vector such that cloning of adaptor-modified cDNA at these sites operably links cDNA to a transcriptional regulatory sequence present in the vector, as described below.

Vector sites for use with the general preferred adaptors described above comprise the following sequences:

-   -   a 5′ site comprising the sequence 5′-C C A N N′₁₀ N′₉ N′₈ N′₇ N         T G G-3′, and a 3 site     -   comprising the sequence 5′-C C A N N₇ N₈ N₉ N₁₀ N T G G-3′;         as read on the same strand, where N₇-N₁₀ correspond to the         nucleotides denoted for adaptors described above, and N is any         nucleotide, preferably a nucleotide selected from the group         consisting. of dAMP, dTMP, dGMP, dCMP, or analogs thereof which         are known in the art, and wherein N′ denotes a nucleotide which         is complementary to N.

Especially preferred vector sites for use with the especially preferred adaptors described above comprise the following sequences:

-   -   a 5′ site comprising the sequence 5′-C C A N T G T G N T G G-3′,         and a 3′ site comprising the     -   sequence 5′-C C A N C A C A N T G G-3′;         as read on the same strand, where N is any nucleotide,         preferably a nucleotide selected from the group consisting of         dAMP, dTMP, dGMP, dCMP, or analogs thereof which are known in         the art.

It will be appreciated that other combinations of adaptors and vector cloning sites may be used to bi-directionally clone random cDNAs. It will be appreciated that other adaptors, comprising other overhangs, which are complementary to the overhangs produced by cleaving vectors at other restriction sites, can be used. What is required is that the adaptors provide for the presentation of identical overhangs at each end of the dscDNA molecule, with non-complementary overhangs being preferred, and that the vector be designed to present identical overhangs at each end of the cDNA insertion site. Non-palindromic sites are desirable, as will be appreciated by those in the art.

Enriching for full-length cDNAs is useful in the art for a number of reasons. Clones having cDNAs that comprise the 5′ UTR allow initiation from proper transcription initiation sites, comprise the translation start site, and allow translation in frame. In addition, full length cDNAs provide 5′ mRNA sequence which often encodes important functional moieties, including targeting signals. In the present methods, synthesis of full length cDNA is additionally desirable because full length cDNA, when digested, provides a larger number of different restriction digest fragments for cloning and expression, and provides for cDNA fragments that are derived from all segments of an mRNA.

Enriching for full length cDNAs can be done by the oligo-capping method (Maruyama and Sugano, Gene 138:171-174 (1994)). This method has been used to obtain libraries with more than 80% full-length clones (Suzuki et al., Gene 200:149-156 (1997)). Regarding the capping method, see also Kato et al. Gene 25, 243-250 (1994). Kits for performing the oligo-capping method are commercially available and may be used in the present methods. For example, see Ambion, FirstChoice™ RLM-RACE kit, catalog #1700, Ambion Inc., Austin, Tex., USA.

The capping method is briefly described as follows. A combination of enzymes may be used to select full length poly(A)+ mRNA and tag their ultimate 5′ ends. Starting from a population of poly(A)+ mRNAs including sequences that are not full length, a phosphatase (such as HK thermolabile phosphatase) can be used to remove the phosphate moiety from mRNAs that are not full length, leaving 5′-OH ends at those mRNAs. Full length poly(A)+ mRNAs are protected due to the 7-methyl-Gppp cap. Tobacco Acid Pyrophosphatase is then used to digest the 7-methyl-Gppp cap, leaving a 5′ phosphate moiety at the 5′ end of the full length mRNA. T4 RNA ligase is then used to tag the full length poly(A)+ mRNAs at their 5′ ends with “oligo-caps”. The oligo caps have a 3′-OH end and thus can be ligated only to poly(A)+ mRNAs displaying a 5′ phosphate moiety. Thus, at the end of this procedure, the full-length mRNAs are tagged at the 5′ end by an oligonucleotide and naturally at the 3′ end by poly(A). Conveniently, the oligonucleotide cap is an RNA oligonucleotide, made by in vitro transcription or made by using an oligonucleotide synthesizer, or a hybrid RNA/DNA oligonucleotide made in an oligonucleotide synthesizer. If desired, a restriction site can be engineered into the oligonucleotide cap. The oligonucleotide cap or the flanking sequence of the vector can also be engineered to include other sequences, including linker sequences for linking first and second nucleic acids, as described herein.

The 5′ CAP attached to the mRNA is transcribed into cDNA. An oligonucleotide comprising the CAP oligo sequence can be annealed to the cDNA CAP and used as a primer for synthesizing the second cDNA strand.

In one embodiment, cDNA synthesis biased towards the 5′ end, as opposed to the 3′ end bias that occurs with poly dT primer, is performed. Random primers are used in combination with CAP oligos and primers. This method provides for capturing-important 5′ encoded functional moieties, described above.

Normalizing cDNA synthesis may also be done. Normalizing is useful because it generally increases the diversity of isolated mRNAs. Normalizing reduces the number of abundant mRNAs while increasing the frequency of rare mRNAs in a sample. For example, abundant mRNAs can be reduced between 100- to 1000-fold, while rare mRNAs can be increased up to 100-fold. Normalized libraries are well known in the art (Soares et al., Proc. Nat'l Acad. Sci. USA-91:9228-9232 (1994); Bonaldo et al., Genome Res. 6:791-806 (1996), Komiya et al., Anal. Biochem. 254:23-30 (1997)).

Typically, normalization is carried out prior to capping and comprises the following steps:

-   -   (i) binding the poly(A)+ mRNAs to oligo d(T) coated substrate;     -   (ii) synthesizing cDNA strands that are complementary to the         mRNAs;     -   (iii) denaturing the cDNA and mRNA strands;     -   (iv) annealing the mRNAs to the substrate bound cDNAs under         conditions such that high abundant mRNAs anneal to the substrate         bound cDNAs and low abundance mRNAs do not anneal; and,     -   (v) collecting a fraction containing the low abundance mRNAs.

These steps may be repeated until the desired level of normalization is achieved in the population of mRNAs.

In a preferred embodiment, cDNA expression vectors comprise cDNA fragments, as described herein. In a further preferred embodiment, cDNA fragments are restriction fragments.

As discussed above, in a preferred embodiment of the methods provided herein, cDNA is digested with selected restriction endonuclease(s). Digestion fragments are modified with adaptors that provide for bi-directional cloning, and modified cDNA fragments are inserted into expression vectors. As described below, cDNA may be inserted in sense or antisense orientation. Further, transcripts from cDNA that is in sense orientation may be translated in frame or out of frame, as further described below. Additionally, transcripts from cDNA that is in antisense orientation may be translated.

Expression vectors additionally comprise control sequences, particularly transcriptional and translational regulatory sequences, which are operably linked to cDNA. The orientation and location of cDNA with respect to these transcriptional and translational regulatory sequences determines whether the cDNA is in sense or antisense configuration, and whether cDNA is translated (read) in frame or out of frame, as further described below.

By transcriptional regulatory sequence (or transcriptional regulatory region, or transcriptional control sequence) is meant a nucleic acid sequence that can regulate transcription from a template strand of nucleic acid by a nucleic acid polymerase. Transcriptional regulatory sequences regulate the expression of an operably linked nucleic acid sequence. The preferred transcriptional regulatory sequence is an RNA polymerase promoter which is positioned relative to a cDNA, or fusion nucleic acid comprising a cDNA, in such a manner that transcription of the cDNA or fusion nucleic acid is initiated.

By translational regulatory sequence (or translation start site sequence, or translation regulatory region) is meant a nucleic acid sequence that can regulate translation from a template nucleic acid sequence by a ribosome or functional components thereof. Translational regulatory sequences regulate the expression of an operably linked coding sequence. The preferred translational regulatory sequence for use in mammalian expression systems comprises the “Kozak” consensus sequence which is known to promote initiation of translation at a starter methionine codon (see Kozak, Cell, 15:1109-1123, 1978).

By “operably linked” is meant that a nucleic acid sequence is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. As another example, operably linked refers to DNA sequences linked so as to be contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. The transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used; for example, transcriptional and translational regulatory nucleic acid sequences from Bacillus are preferably used to express cDNA in Bacillus. Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells.

In general, the transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences. In a preferred embodiment, the regulatory sequences include a promoter and transcriptional start and stop sequences.

Promoter sequences encode either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters. Hybrid promoters, which combine elements of more than one promoter, are also known in the art, and are useful in the present invention.

Particularly preferred for use in the present expression vectors is the composite promoter CRU5, which comprises a CMV promoter fused to the transcriptional start site of the MMLV R-U5 region of the LTR (Lorens et al., Mol. Ther., 1:438-447, 2000).

A preferred inducible promoter for use in the present invention is a tet-inducible promoter comprising multiple copies of the tet operon operably linked to a minimal human CMV promoter (for example, see Gossen et al., PNAS 89:5547-5551, 1992).

In a preferred embodiment, the cDNA expression vector libraries provided herein each comprise three different types of cDNA expression vectors which differ in the orientation and translational frame of the cDNA inserts therein and in the expression products they produce. Each vector comprises a cDNA which is operably linked to transcriptional and translational regulatory sequences in one of three ways; in sense orientation and in frame; in sense orientation and out of frame (frameshifted); and in antisense orientation. Libraries provided herein comprise a mixture of such vectors.

It will be appreciated that the digestion of random cDNA with restriction endonucleases, and modification of random cDNA restriction fragments with adaptors that provide for bi-directional cloning into expression vectors, provides for the synthesis of these three types of vectors in a single process, which is desirable.

It will also be appreciated that many different cDNA expression vector species are provided by the present methods. cDNAs inserted in sense orientation are translated in one of three possible frames. One frame is the same as that of the native ORF of the corresponding mRNA, while the other two frames provide for the expression of “random” polypeptides. Of course the sequence of such random polypeptides is dictated by the sequence of cDNA, which is in turn dictated by the sequence of template mRNA. By “random” is meant that the amino acid sequence of the polypeptide expression product does not correspond to the amino acid sequence encoded by the native ORF.

In addition, cDNA inserted in antisense orientation may also be translated. Translation of antisense nucleic acid provides “random polypeptides” as referred to herein, though the sequence of these polypeptides is also dictated by the sequence of template mRNA.

Detailed descriptions of the orientation of cDNA, the operable linkage of cDNAs to transcription and translation regulatory sequences, and the expression products produced by the three different types of cDNA expression vectors, is presented below in reference to the preferred embodiment of retroviral cDNA expression vectors.

Expression vectors provided herein may comprise additional elements. For example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. Furthermore, for some integrating expression vectors, the expression vector contains at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art.

Expression vectors may also include cDNA fusion partners. “Fusion partner” as used herein can refer to nucleic acids and peptides. Fusion partner can refer both to the fusion partner encoding nucleic acid sequence in an expression vector, and a nucleic acid or peptide expression product of the encoding sequence. The use of fusion partners is particularly desirable when using cDNA libraries to screen for bioactve agents that can modulate cell phenotype in a desirable way, as described below.

In a preferred embodiment, cDNAs are fused to fusion partners. In another preferred embodiment, cDNAs are linked to fusion partners by linkers, as described below. In this embodiment, cDNAs may be tethered to fusion partners, or may be separate or separable from fusion partners, as described below.

cDNA may be positioned 5′, 3′, or within a fusion partner, as described below. By “fusion partner” or “functional group” herein is meant a sequence that is associated with a cDNA expression product, including nucleic acids and peptides, that confers upon all members of the library in that class a common function or ability.

In the discussion of fusion partners that follows, cDNA expression products are sometimes referred to as candidate bioactive agents, candidate agents, candidate peptides, or candidate nucleic acids, stemming from their use in methods of screening for bioactive agents, described below.

Fusion partners can be heterologous (i.e. not native to the host cell), or synthetic (not native to any cell). Suitable fusion partners include, but are not limited to: a) presentation structures, as defined below, which provide the candidate bioactve agents in a conformationally restricted or stable form; b) targeting sequences, defined below, which allow the localization of the candidate bioactive agent into a subcellular or extracellular compartment; c) rescue sequences as defined below, which allow the purification or isolation of either the candidate bioactive agents or the nucleic acids encoding them; d) stability sequences, which confer stability of protection from degradation to the candidate bioactive agent or the nucleic acid encoding it, for example resistance to proteolytic degradation; e) dimerization sequences, to allow for peptide dimerization; f) label sequences; or g) any combination of a), b), c), d), e), and f), as well as linker sequences as needed.

In a preferred embodiment, the fusion partner is a presentation structure. By “presentation structure” or grammatical equivalents herein is meant a sequence, which, when fused to candidate bioactive agents, causes the candidate agents to assume a conformationally restricted form. Proteins interact with each other largely through conformationally constrained domains. Although small peptides with freely rotating amino and carboxyl termini can have potent functions as is known in the art, the conversion of such peptide structures into pharmacologic agents is difficult due to the inability to predict side-chain positions for peptidomimetic synthesis. Therefore the presentation of cDNA-encoded peptides in conformationally constrained structures will benefit both the later generation of pharmaceuticals and will also likely lead to higher affinity interactions of the peptide with the target protein. This fact has been recognized in the combinatorial library generation systems using biologically generated short peptides in bacterial phage systems. A number of workers have constructed small domain molecules in which one might present randomized peptide structures.

Synthetic presentation structures are usually peptides, i.e. artificial polypeptides, and are capable of presenting a candidate peptide as a conformationally-restricted domain. Generally such presentation structures comprise a first portion joined to the N-terminal end of the candidate peptide, and a second portion joined to the C-terminal end of the peptide; that is, the peptide is inserted into the presentation structure, although variations may be made. To increase the functional isolation of the candidate peptide, the presentation structures are selected or designed to have minimal biologically activity when expressed in the target cell. The use of presentation structures is particularly desirable in the present invention as the expression products of the present vectors include random peptides that lack the integral domains of mRNA-encoded polypeptides and the stability conferred thereby.

Preferred presentation structures maximize accessibility to the cDNA-encoded peptide by presenting it on an exterior loop. Accordingly, suitable presentation structures include, but are not limited to, minibody structures, loops on beta-sheet turns and coiled-coil stem structures in which residues not critical to structure are found, zinc-finger domains, cysteine-linked (disulfide) structures, transglutaminase linked structures, cyclic peptides, B-loop structures, helical barrels or bundles, leucine zipper motifs, etc.

In a preferred embodiment, the presentation structure is a coiled-coil structure, allowing the presentation of the candidate peptide on an exterior loop. See, for example, Myszka et al., Biochem. 33:2362-2373 (1994), hereby incorporated by reference). Using this system investigators have isolated peptides capable of high affinity interaction with the appropriate target.

In a preferred embodiment, the presentation structure is a minibody structure. A “minibody” is essentially composed of a minimal antibody complementarity region. The minibody presentation structure generally provides two sequence replacement regions that in the folded protein are presented along a single face of the tertiary structure. See for example Bianchi et al., J. Mol. Biol. 236(2):649-59 (1994), and references cited therein, all of which are incorporated by reference). Investigators have shown this minimal domain is stable in solution and have used phage selection systems in combinatorial libraries to select minibodies with peptide regions exhibiting high affinity, Kd=10⁻⁷, for the pro-inflammatory cytokine IL-6.

In a preferred embodiment, the presentation structure is a sequence that contains generally two cysteine residues, such that a disulfide bond may be formed, resulting in a conformationally constrained sequence. This embodiment is particularly preferred when secretory targeting sequences are used. As will be appreciated by those in the art, any number of candidate peptides, with or without spacer sequences, may be flanked with cysteine residues.

In a preferred embodiment, the presentation structure can be a protein, such as a reporter gene. For example, fusion of peptides to reporter proteins such as GFP have been shown to confer conformational stability.

In a preferred embodiment, the fusion partner is a targeting sequence. As will be appreciated by those in the art, the localization of proteins within a cell is a simple method for increasing effective concentration and determining function. For example, RAF1 when localized to the mitochondrial membrane can inhibit the anti-apoptotic effect of BCL-2. Similarly, membrane bound Sos induces Ras mediated signaling in T-lymphocytes. These mechanisms are thought to rely on the principle of limiting the search space for ligands, that is to say, the localization of a protein to the plasma membrane limits. the search for its ligand to that limited dimensional space near the membrane as opposed to the three dimensional space of the cytoplasm. Alternatively, the concentration of a protein can also be simply increased by nature of the localization. Shuttling the proteins into the nucleus confines them to a smaller space thereby increasing concentration. Finally, the ligand or target may simply be localized to a specific compartment, and inhibitors must be localized appropriately.

Targetting sequences may serve as surrogate signals for cDNA expression products that lack signal sequences native to corresponding full length transcription or translation products. Alternatively, targeting sequences may deliver cDNA expression products to subcellular locations in which full length transcription or translation products are not found.

Suitable targeting sequences include, but are not limited to, binding sequences capable of causing binding of the cDNA fragment expression product to a predetermined molecule or class of molecules while retaining bioactivity of the expression product, (for example by using enzyme inhibitor or substrate sequences to target a class of relevant enzymes); sequences signaling selective degradation, of itself or co-bound proteins; and signal sequences capable of constitutively localizing the candidate expression products to a predetermined cellular locale, including a) subcellular locations such as the Golgi, endoplasmic reticulum, nucleus, nucleoli, nuclear membrane, mitochondria, chloroplast, secretory vesicles, lysosome, and cellular membrane; and b) extracellular locations via a secretory signal. Particularly preferred is localization to either subcellular locations or to the outside of the cell via secretion.

In a preferred embodiment, the targeting sequence is a nuclear localization signal (NLS). NLSs are generally short, positively charged (basic) domains that serve to direct the entire protein in which they occur to the cell's nucleus. Numerous NLS amino acid sequences have been reported including single basic NLS's such as that of the SV40 (monkey virus) large T Antigen (Pro Lys Lys Lys Arg Lys Val), Kalderon (1984), et al., Cell, 39:499-509; the human retinoic acid receptor-β nuclear localization signal (ARRRRP); NFκB p50 (EEVQRKRQKL; Ghosh et al., Cell 62:1019 (1990); NFκB p65 (EEKRKRTYE; Nolan et al., Cell 64:961 (1991); and others (see for example Boulikas, J. Cell. Biochem. 55(1):32-58 (1994), hereby incorporated by reference) and double basic NLS's exemplified by that of the Xenopus (African clawed toad) protein, nucleoplasmin (Ala Val Lys Arg Pro Ala Ala Thr Lys Lys Ala Gly Gln Ala Lys Lys Lys Lys Leu Asp), Dingwall, et al., Cell, 30:449-458, 1982 and Dingwall, et al., J. Cell Biol., 107:641-849; 1988). Numerous localization studies have demonstrated that NLSs incorporated in synthetic peptides or grafted onto reporter proteins not normally targeted to the cell nucleus cause these peptides and-reporter proteins to be concentrated in the nucleus. See, for example, Dingwall, and Laskey, Ann, Rev. Cell Biol., 2:367-390, 1986; Bonnerot, et al., Proc. Natl. Acad. Sci. USA, 84:6795-6799, 1987; Galileo, et al., Proc. Natl. Acad. Sci. USA, 87:458-462, 1990.

In a preferred embodiment, the targeting sequence is a membrane anchoring signal sequence. This is particularly useful since many parasites and pathogens bind to the membrane, in addition to the fact that many intracellular events originate at the plasma membrane. Thus, membrane-bound peptide libraries are useful for both the identification of important elements in these processes as well as for the discovery of effective inhibitors. The invention provides methods for presenting the candidate agent extracellularly or in the cytoplasmic space. For extracellular presentation, a membrane anchoring region is provided at the carboxyl terminus of the peptide presentation structure. The candidate agent is expressed on the cell surface and presented to the extracellular space, such that it can bind to other surface molecules (affecting their function) or molecules present in the extracellular medium. The binding of such molecules could confer function on the cells expressing a peptide that binds the molecule. The cytoplasmic region could be neutral or could contain a domain that, when the extracellular candidate agent is bound, confers a function on the cells (activation of a kinase, phosphatase, binding of other cellular components to effect function). Similarly, the candidate agent could be contained within a cytoplasmic region, and the transmembrane region and extracellular region remain constant or have a defined function.

Membrane-anchoring sequences are well known in the art and are based on the genetic geometry of mammalian transmembrane molecules. Peptides are inserted into the membrane based on a signal sequence (designated herein as ssTM) and require-a hydrophobic transmembrane domain (herein TM). The transmembrane proteins are inserted into the membrane such that the regions encoded 5′ of the transmembrane domain are extracellular and the sequences 3′ become intracellular. Of course, if these transmembrane domains are placed 5′ of the candidate agent region, they will serve to anchor it as an intracellular domain, which may be desirable in some embodiments. ssTMs and TMs are known for a wide variety of membrane bound proteins, and these sequences may be used accordingly, either as pairs from a particular protein or with each component being taken from a different protein, or alternatively, the sequences may be synthetic, and derived entirely from consensus as artificial delivery domains.

As will be appreciated by those in the art, membrane-anchoring sequences, including both ssTM and TM, are known for a wide variety of proteins and any of these may be used. Particularly preferred membrane-anchoring sequences include, but are not limited to, those derived from CD8, ICAM-2, IL-8R, CD4 and LFA-1.

Useful sequences include sequences from: 1) class I integral membrane proteins such as IL-2 receptor beta-chain (residues 1-26 are the signal sequence, 241-265 are the transmembrane residues; see Hatakeyama et al., Science 244:551 (1989) and von Heijne et al, Eur. J. Biochem. 174:671 (1988)) and insulin receptor beta chain (residues 1-27 are the signal, 957-959 are the transmembrane domain and 960-1382 are the cytoplasmic domain; see Hatakeyama, supra, and Ebina et al., Cell 40:747 (1985)); 2) class 11 integral membrane proteins such as neutral endopeptidase (residues 29-51 are the transmembrane domain, 2-28 are the cytoplasmic domain; see Malfroy et al., Biochem. Biophys. Res. Commun. 144:59 (1987)); 3) type III proteins such as human cytochrome P450 NF25 (Hatakeyama, supra); and 4) type IV proteins such as human P-glycoprotein (Hatakeyama, supra). Particularly preferred are CD8 and ICAM-2. For example, the signal sequences from CD8 and ICAM-2 lie at the extreme 5′ end of the transcript. These consist of the amino acids 1-32 in the case of CD8 (MASPLTRFLSLNLLLLGESILGSGEAKPQAP; Nakauchi et al., PNAS USA 82:5126 (1985) and 1-21 in the case of ICAM-2 (MSSFGYRTLTVALFTLICCPG; Staunton et al., Nature (London) 339:61 (1989)). These leader sequences deliver the construct to the membrane while the hydrophobic transmembrane domains, placed 3′ of the candidate agent region, serve to anchor the construct in the membrane. These transmembrane domains are encompassed by amino acids 145-195 from CD8 (PQRPEDCRPRGSVKGTGLDFACDIYIWAPLAGICVALLLSLIITLICYHSR; Nakauchi, supra) and 224-256 from ICAM-2 (MVIIVTVVSVLLSLFVTSVLLCFIFGQHLRQQR; Staunton, supra).

Alternatively, membrane anchoring sequences include the GPI anchor, which results in a covalent bond between the molecule and the lipid bilayer via a glycosyl-phosphatidylinositol bond for example in DAF (PNKGSGTTSGTTRLLSGHTCFTLTGLLGTLVTMGLLT, with the bolded serine the site of the anchor; see Homans et al., Nature 333(6170):269-72 (1988), and Moran et al., J. Biol. Chem. 266:1250 (1991)). In order to do this, the GPI sequence from Thy-1 can be cassetted 3′ of the candidate agent region in place of a transmembrane sequence.

Similarly, myristylation sequences can serve as membrane anchoring sequences. It is known that the myristylation of c-src recruits it to the plasma membrane. This is a simple and effective method of membrane localization, given that the first 14 amino acids of the protein are solely responsible for this function: MGSSKSKPKDPSQR (see Cross et al., Mol. Cell. Biol. 4(9):1834 (1984); Spencer et al., Science 262:1019-1024 (1993), both of which are hereby incorporated by reference). This motif has already been shown to be effective in the localization of reporter genes and can be used to anchor the zeta chain of the TCR. This motif is placed 5′ of the candidate agent region in order to localize the construct to the plasma membrane. Other modifications such as palmitoylation can be used to anchor constructs in the plasma membrane; for example, palmitoylation sequences from the G protein-coupled receptor kinase GRK6 sequence (LLQRLFSRQDCCGNCSDSEEELPTRL, with the bold cysteines being palmitolyated; Stoffel et al., J. Biol. Chem 269:27791 (1994)); from rhodopsin (KQFRNCMLTSLCCGKNPLGD; Barnstable et al., J. Mol. Neurosci. 5(3):207 (1994)); and the p21 H-ras 1 protein (LNPPOESGPGCMSCKCVLS; Capon et al., Nature 302:33 (1983)).

In a preferred embodiment, the targeting sequence is a lysozomal targeting sequence, including, for example, a lysosomal degradation sequence such as Lamp2 (KFERQ; Dice, Ann. N.Y. Acad. Sci. 674:58 (1992); or lysosomal membrane sequences from Lamp-1 (MLIPIAGFFALAGLVUVLIAYLIGRKRSHAGYQTI, Uthayakumar et al., Cell. Mol. Biol. Res. 41:405 (1995)) or Lamp-2 (LVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF, Konecki et la., Biochem. Biophys. Res. Comm. 205:1-5 (1994), both of which show the transmembrane domains in italics and the cytoplasmic targeting signal underlined).

Alternatively, the targeting sequence may be a mitochondrial localization sequence, including mitochondrial matrix sequences (e.g. yeast alcohol dehydrogenase III; MLRTSSLFTRRVQPSLFSRNILRLQST; Schatz, Eur. J. Biochem. 165:1-6 (1987)); mitochondrial inner membrane sequences (yeast cytochrome c oxidase subunit IV; MLSLRQSIRFFKPATRTLCSSRYLL; Schatz, supra); mitochondrial intermembrane space sequences (yeast cytochrome c1; MFSMLSKRWAQRTLSKSFYSTATGAASKSGKLTQKLVTAGVAAAGITASTLLYADSLTAEAMTA; Schatz, supra) or mitochondrial outer membrane sequences (yeast 70 kD outer membrane protein; MKSFITRNKTAILATVMTGTAIGAYYYYNQLQQQQQRGKK; Schatz, supra).

The target sequences may also be endoplasmic reticulum sequences, including the sequences from calreticulin (KDEL; Pelham, Royal Society London Transactions B; 1-10 (1992)) or adenovirus E3/19K protein (LYLSRRSFIDEKKMP; Jackson et al., EMBO J. 9:3153 (1990).

Furthermore, targeting sequences also include peroxisome sequences (for example, the peroxisome matrix sequence from Luciferase; SKL; Keller et al., PNAS USA 4:3264 (1987)); farnesylation sequences (for example, P21 H-ras 1; LNPPDESGPGCMSCKCVLS, with the bold cysteine farnesylated; Capon, supra); geranylgeranylation sequences (for example, protein rab-5A; LTEPTQPTRNQCCSN, with the bold cysteines geranylgeranylated; Farnsworth, PNAS USA 91:11963 (1994)); or destruction sequences (cyclin B1; RTALGDIGN; Klotzbucher et al., EMBO J. 1:3053 (1996)).

In a preferred embodiment, the targeting sequence is a secretory signal sequence capable of effecting the secretion of the candidate translation product. There are a large number of known secretory signal sequences which are placed 5′ to the variable peptide region, and are cleaved from the peptide region to effect secretion into the extracellular space. Secretory signal sequences and their transferability to unrelated proteins are well known, e.g., Silhavy, et al. (1985) Microbiol. Rev. 49, 398-418. This is particularly useful to generate a peptide capable of binding to the surface of, or affecting the physiology of, a target cell that is other than the host cell, e.g., the cell infected with the retrovirus. In a preferred approach, a fusion product is configured to contain, in series, secretion signal peptide-presentation structure-candidate agent-presentation structure, In this manner, target cells grown in the vicinity of cells caused to express the library of peptides, are bathed in secreted peptide. Target cells exhibiting a physiological change in response to the presence of a peptide, e.g., by the peptide binding to a surface receptor or by being internalized and binding to intracellular targets, and the secreting cells are localized by any of a variety of selection schemes and the peptide causing the effect determined. Exemplary effects include variously that of a designer cytokine (e.g., a stem cell factor capable of causing hematopoietc stem cells to divide and maintain their totpotental), a factor causing cancer cells to undergo spontaneous apoptosis, a factor that binds to the cell surface of target cells and labels them specifically, etc.

Suitable secretory sequences are known, including signals from IL-2 (MYRMQLLSCIALSLALVTNS; Villinger et al., J. Immunol. 155:3946 (1995)), growth hormone (MATGSRTSLLLAFGLLCLPWLQEGSAFPT; Roskam et al., Nucleic Acids Res. 7:30 (1979)); preproinsulin (MALWMRLLPLLALLALWGPDPAAAFVN; Bell et al., Nature 284:26 (1980)); and influenza HA protein (MKAKLLVLLYAFVAGDQI; Sekiwawa et al., PNAS 80:3563)), with cleavage between the non-underlined-underlined junction. A particularly preferred secretory signal sequence is the signal leader sequence from the secreted cytokine IL-4, which comprises the first 24 amino acids of IL-4 as follows: MGLTSQLLPPLFFLLACAGNFVHG.

In a preferred embodiment, the fusion partner is a rescue sequence. A rescue sequence is a sequence which may be used to purify or isolate either the candidate agent or the nucleic acid encoding it. Thus, for example, peptide rescue sequences include purification sequences such as the His₆ tag for use with Ni affinity columns and epitope tags for detection, immunoprecipitation or FACS (fluoroscence-activated cell sorting). Suitable epitope tags include myc (for use with the commercially available 9E10 antibody), the BSP biotinylation target sequence of the bacterial enzyme BirA, flu tags, lacZ, and GST.

Alternatively, the rescue sequence may be a unique oligonucleotide sequence which serves as a probe target site to allow the quick and easy isolation of the cDNA, via PCR, related techniques, or hybridization.

In a preferred embodiment, the fusion partner is a stability sequence to confer stability to the candidate bioactive agent or the nucleic acid encoding it. Thus, for example, candidate peptides may be stabilized by the incorporation of glycines after the initiation methionine (MG or MGG0), for protection of the peptide to ubiquitination as per Varshavsky's N-End Rule, thus conferring long half-life in the cytoplasm. Similarly, two prolines at the C-terminus provide for candidate peptides that are largely resistant to carboxypeptidase action. The presence of two glycines prior to the prolines imparts flexibility and prevents structure initiating events in the di-proline from being propagated into the candidate peptide structure. Thus, preferred stability sequences are as follows: MG(X)_(n)GGPP, where X is any amino acid and n is an integer of at least four.

In one embodiment, the fusion partner is a dimerization sequence. A dimerization sequence allows the non-covalent association of one candidate peptide to another candidate peptide, with sufficient affinity to remain associated under normal physiological conditions. This effectively allows small libraries of candidate peptides (for example, 10⁴) to become large libraries if two peptides per cell are generated which then dimerize, to form an effective library of 10⁸ (10⁴×10⁴). It also allows the formation of longer candidate peptides, if needed, or more structurally complex candidate peptide molecules. The dimers may be homo- or heterodimers. See for example U.S. Ser. No. 09/285,912, incorporated herein in its entirety by reference.

Dimerization sequences may be a single sequence that self-aggregates, or two sequences, each of which is generated in a different cDNA expression vector construct. That is, nucleic acids encoding both a first candidate peptide with dimerizaton sequence 1, and a second candidate peptide with dimerization sequence 2, such that upon introduction into a cell and expression of the nucleic acid, dimerization sequence 1 associates with dimerization sequence 2 to form a new candidate peptide structure.

Suitable dimerization sequences will encompass a wide variety of sequences. Any number of protein-protein interaction sites are known (for example, see description of dimerization sequences set forth in WO 99/51625, incorporated herein by reference). In addition, dimerization sequences may also be elucidated using standard methods such as the yeast two hybrid system, traditional biochemical affinity binding studies, or even using the present methods.

In a preferred embodiment, the fusion partner is a selection gene or a reporter gene.

By “reporter gene” or “selection gene” or grammatical equivalents herein is meant a gene that by its presence in a cell (i.e. upon expression) can allow the cell to be distinguished from a cell that does not contain the reporter gene. Reporter genes can be classified into several different types, including detection genes, survival genes, death genes and cell cycle genes.

In the screening methods described below, which use cDNA libraries, expression of the cDNA causes the effect distinguishing between cells expressing the reporter gene and those that do not. As is more fully outlined below, additional components, such as substrates, ligands, etc., may be additionally added to allow selection or sorting on the basis of the reporter gene.

In an especially preferred embodiment, the reporter gene encodes a detectable protein that can be used as a direct label, for example a detection gene for sorting the cells or for cell enrichment by FACS. In this embodiment, the protein product of the reporter gene itself can serve to distinguish cells that are expressing the reporter gene. In this embodiment, suitable reporter genes include those encoding a luciferase gene from firefly, Renilla, or Ptiolosarcus, as well as genes encoding green fluorescent protein (GFP; Chalfie, M. et al. (1994) Science 263: 802-05; and EGFP; Clontech—Genbank Accession Number U55762 ), blue fluorescent protein (BFP; Quantum Biotechnologies, Inc. 1801 de Maisonneuve Blvd. West, 8th Floor, Montreal (Quebec) Canada H3H 1J9; Stauber, R. H. (1998) Biotechniques 24: 462-71; Heim, R. et al. (1996) Curr. Biol. 6: 178-82), enhanced yellow fluorescent protein (EYFP; 1. Clontech Laboratories, Inc., 1020 East Meadow Circle, Palo Alto, Calif. 94303), luciferase (Kennedy, H. J. et al. (1999) J. Biol. Chem. 274: 13281-91), Renilla reniformis GFP (WO 99/49019), Ptilosarcus gumeyi GFP (WO 99/49019; U.S. Ser. No. 60/164,592; U.S. Ser. No. 09/710,058; U.S. Ser. No. 60/290,287), Renilla mulleris GFP (WO 99/49019; U.S. Ser. No. 60/164,592; U.S. Ser. No. 09/710,058; U.S. Ser. No. 60/290,287); GFP homologue from Anthozoa species (Nat. Biotech., 17:969-973, 1999); β-galactosidase (Nolan, G. et al. (1988) Proc. Natl. Acad. Sci. USA 85: 2603-07), β-glucouronidase (Jefferson, R. A. et al. (1987) EMBO J. 6: 3901-07; Gallager, S., “GUS Protocols: Using the GUS Gene as a reporter of gene expression,” Academic Press, Inc., 1992), and secreted form of human placental alkaline phosphatase, SEAP (Cullen, B. R. et al. (1992) Methods Enzymol. 216: 362-68). In a preferred embodiment, the codons of the reporter genes are optimized for expression within a particular organism, especially mammals, and particularly preferred for humans (see Zolotukhin, S. et al. (1996) J. Virol. 70: 4646-54; U.S. Pat. Nos. 5,968,750; 6,020,192; U.S. Ser. No. 60/290,287, all of which are expressly incorporate by reference).

The green fluorescent protein from Aequorea Victoria is a 238 amino acid protein. The crystal structure of the protein and of several point mutants has been solved (Ormo et al., Science 273, 1392-5, 1996; Yang et al., Nature Biotechnol. 14, 1246-51, 1996). The fluorophore, consisting of a modified tripeptide, is buried inside a relatively rigid beta-can structure, where it is almost completely protected from solvent access. The fluorescence of this protein is sensitive to a number of point mutations (Phillips, G. N., Curr. Opin. Struct: Biol. 7, 821-27, 1997). The fluorescence appears to be a sensitive indication of the preservation of the native structure of the protein, since any disruption of the structure allowing solvent access to the fluorophoric tripeptide will quench the fluorescence.

The Renilla GFP used in the present invention preferably has significant homology to the wild-type Renilla GFP protein as depicted in WO 99/49019, hereby incorporated by reference in its entirety.

Alternatively, the reporter gene encodes a protein that will bind a label that can be used as the basis of the cell enrichment (sorting); that is, the reporter gene serves as an indirect label or detection gene. In this embodiment, the reporter gene should encode a cell-surface protein. For example, the reporter gene may be any cell-surface protein not normally expressed on the surface of the cell, such that secondary binding agents serve to distinguish cells that contain the reporter gene from those that do not. Alternatively, albeit non-preferably, reporters comprising normally expressed cell-surface proteins could be used, and differences between cells containing the reporter construct and those without could be determined. Thus, secondary binding agents bind to the reporter protein. These secondary binding agents are preferably labeled, for example with fluorophores, and can be antibodies, haptens, etc. For example, fluorescently labeled antibodies to the reporter gene can be used as the label. Similarly, membrane-tethered streptavidin could serve as a reporter gene, and fluorescently-labeled biotin could be used as the label, i.e. the secondary binding agent. Alternatively, the secondary binding agents need not be labeled as long as the secondary binding agent can be used to distinguish the cells containing the construct; for example, the secondary binding agents may be used in a column, and the cells passed through, such that the expression of the reporter gene results in the cell being bound to the column, and a lack of the reporter gene (i.e. inhibition), results in the cells not being retained on the column. Other suitable reporter proteins/secondary labels include, but are not limited to, antigens and antibodies, enzymes and substrates (or inhibitors), etc.

In one embodiment, the reporter gene is a survival gene that serves to provide a nucleic acid (or encode a protein) without which the cell cannot survive, such as drug resistance genes. In this embodiment, expressing the survival gene allows selection of cells by identifying cells that survive, for example in presence of a selection drug. Examples of drug resistance genes include, but are not limited to, puromycin resistance (puromycin-N-acetyl-transferase) (de la Luna, S. and Ortin, J. Methods Enzymol. (1992) 216:376-385), G418 neomycin resistance gene, hygromycin resistance gene (hph), and blasticidine resistance genes (bsr, brs, and BSD)(Pere-Gonzalez, et al., Gene (1990).86: 129-134; Izumi et al.,.Exp. Cell Res (1991) 197: 229-233; Itaya et al. (1990) J. Biochem. 107: 799-801; Kimura, et al. Mol. Gen. Genet. (1994) 242:121-129). In addition, generally applicable survival genes are the family of ATP-binding cassette transporters, including multiple drug resistance gene (MDR1) (see Kane et. al. (1988) Mol. Cell. Biol. 8: 3316 and Choi et al. (1988) Cell 53: 519), multidrug resistance associated proteins (MRP) (Bera T. K. et al. (2001) Mol. Med. 7:509-16), and breast cancer associated protein (BCRP or MXR) (Tan B. et al. (2000) Curr. Opin. Oncol. 12:450-8). When expressed in cells, these selectable genes can confer resistance to a variety of anti-cancer drugs (i.e. methotrexate, colchicine, tamoxifen, mitoxanthrone, and doxorubicin).

In one embodiment, the reporter gene is a death gene, which encodes a protein that causes the cells to die. Death genes fall into two basic categories: death genes that encode death proteins that require a death ligand to kill the cells, and death genes that encode death proteins that kill cells as a result of high expression within the cell, and do not require the addition of any death ligand. In one embodiment, cell death requires a two-step process: the expression of the death gene and induction of the death phenotype with a signal or ligand, such that the cells may be grown up expressing the death gene, and then induced to die. A number of death genes/ligand pairs are known, including, but not limited to, the Fas receptor and Fas ligand (Bodmer, et al. (1997) J. Biol. Chem. 272:18827-18833; Gonzalez-Cuadrado, et al. (1997) Kidney Int. 51:1739-1746; Muruva, et al. (1997) Hum Gene Ther., 8:955); p450 and cyclophosphamide (Chen, et al. (1997) Cancer Res 57:4830-4837); thymidine kinase and gangcylovir (Stone, R. (1992) 256:1513), tumor necrosis factor (TNF) receptor and TNF. Alternatively, the death gene need not require a ligand, and death results from high expression of the gene; for example, the overexpression of a number of programmed cell death (PCD) proteins are known to cause cell death, including, but not limited to, caspases, bax, TRADD, FADD, BADD, SCK, MEK, etc. Still other death genes require only moderate levels of expression to be lethal to a cell, and are more aptly referred to as toxins. These genes encode products including, but not limited to, anthrax toxin (Pannifer et al., Nature 414(6860):229-233 (2001)), botulinum toxin, pertussis toxin, cholera toxin, Clostridium dificile toxin A & B (Just et al., Int. J. Med. Microbiol. 291(4):243-250 (2001)), α-toxin, tetanus toxin, hemolysin (Worsham et al., Biochem. 40(45):3607-3616 (2001)) and cytolethal distending toxins (Cortes-Bratti et al., Toxicon. 39(11):729-736 (2001)).

In one embodiment, the reporter gene is a cell cycle gene, that is, a gene that causes alterations in the cell cycle. For example, Cdk interacting protein p21 (see Harper et al. (1993) Cell 75: 805-816), which inhibits cyclin dependent kinases, does not cause cell death but causes cell-cycle arrest. Thus, expressing the p21 allows selection for regulators of promoter activity or regulators of p21 activity based on detecting cells that grow out much more quickly due to low p21 activity, either through inhibiting promoter activity or inactivation of p21 protein activity. As will be appreciated by those in the art, it is also possible to configure the system to select cells based on their inability to grow out due to increased p21 activity.

In a preferred embodiment, the fusion partner includes a linker or tethering sequence.

Linkers may comprise nucleic acid encoding protein to form a protein linker or tether. Alternatively, linkers may be separation sequences that provide for the expression of separate proteins.

Linker sequences between various targeting sequences (for example, membrane targeting sequences) and the other components of the constructs (such as the candidate agents) may be desirable to allow the candidate agents to interact with potential targets unhindered. For example, when the candidate bioactive agent is a peptide, useful linkers include glycine-serine polymers (including, for example, (GS)_(n), (GSGGS)_(n) and (GGGS)_(n), where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, and other flexible linkers such as the linker for the shaker potassium channel, and a large variety of other flexible linkers, as will be appreciated by those in the art. Glycine-serine polymers are preferred since both of these amino acids are relatively unstructured, and therefore may be able to serve as a neutral linker between components. Secondly, serine is hydrophilic and therefore able to solubilize what could be a globular glycine chain. Third, similar chains have been shown to be effective in joining subunits of recombinant proteins such as single chain antibodies.

In one embodiment, the linker is a separation sequence. Separation sequences include, but are not limited to, IRES, type 2a site, and peptidase cleavage sites, all of which are described below in reference to the preferred embodiment of retroviral vectors.

In addition, the fusion partners, including presentation structures, may be modified, randomized, and/or matured to alter the presentation orientation of the candidate agent. For example, determinants at the base of the loop may be modified to slightly modify the internal loop peptide tertiary structure, while maintaining the amino acid sequence of the cDNA encoded polypeptide moiety.

In one embodiment, combinations of fusion partners are used. Thus, for example, any number of combinations of presentation structures, targeting sequences, rescue sequences, and stability sequences may be used, with or without linkers.

In one aspect, the cDNA expression vectors provided herein are lentviral vectors. As is known, lentiviruses, such as HIV virus, are capable of infecting both dividing and non-dividing cells. Vectors based on HIV viruses and packaging methods are known in the art (see Miyoshi, H. (1998) J. Virol. 72: 8150-57; Zufferey, R. (1998) J. Virol. 72: 9873-80; Iwakuma, T. (1999) Virology 261: 120-32; Xu, K. (2001) Mol. Ther. 3: 97-104).

In one aspect of the invention, the cDNA expression vectors provided herein are retroviral vectors. Accordingly, provided herein are retroviral cDNA expression vector libraries. Each library comprises a plurality of retroviral cDNA expression vectors. Each library further comprises three different types of retroviral cDNA expression vectors which differ in the orientation and translational frame of the cDNA inserts therein, as well as in the expression products produced thereby.

As used herein, “retroviral vector” refers to a retroviral genome which is other than a naturally occurring retroviral genome.

By retroviral genome herein is meant an RNA which is capable of being reverse transcribed (to DNA) and incorporated into the genome of a cell infected by a retroviral particle comprising the retroviral genome via the activity of the enzymatic proteins of the particle. Complete retroviral genomic maps have been produced for many different retroviruses (see Appendix 2: Retroviral taxonomy, protein structures, sequences, and genetc maps. In “Retroviruses”, (Coffin et al., eds.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1997), pp. 757-805), incorporated herein), and retrovirus replication cycle has been extensively studied (see John M. Coffin, Retroviridae: The Viruses and Their Replication, In “Virology”, Volume 2, Third Edition (Fields et al., eds.), Lippincot-Raven Publishers, Philadelphia, Pa. (1996), pp. 1767-1847, also incorporated herein). Retroviral genomes and vectors useful in the present invention may be derived from any retrovirus. The skilled artisan will appreciate that the selection of a retrovirus for use in the invention will be based largely upon the intended used, particularly on the type of cell to be infected by a retroviral particle comprising a retroviral genome of the invention, as described below. One preferred retrovirus upon which a retroviral genome of the invention is based is the Murine leukemia virus (MuLV).

In a preferred embodiment, the retroviral genome comprises a 5′ long terminal repeat (LTR). The 5′ LTR is generally the sequence at the 5′ end of the retroviral genomic. RNA which encodes un-translated sequences when the retroviral genome has been incorporated into the genome of the host. In a preferred embodiment, the 5′ LTR comprises a terminal redundant region (R region) and a 5′ unique region (U5 region).

In a preferred embodiment, the retroviral genome comprises a 3′ LTR, which is generally the 3′ end of the retroviral genomic RNA which encodes un-translated sequences. Preferably, the 3′ LTR comprises an R region (identical to the R region found at the 5′ end) and a 3′ unique region (U3). Preferably, the 3′ LTR also comprises a poly adenosine terminal sequence (poly-A tail). In a preferred embodiment the poly-A tail is from 20-60 residues long, preferably about 40 residues long.

In a preferred embodiment, the retroviral genome is modified MMLV genome and comprises a composite CMV promoter fused to the transcriptional start site of the MMLV R-U5 region of the LTR, an extended packaging sequence, and deletion of the MMLV Gag start ATG. For example, see Lorens et. al., Mol. Therapy, 1:438-447, 2000. This recombinant promoter is sometimes referred to herein as “CRU5”.

The different components of the retroviral genome have been widely studied and are well known in the art (see Coffin, above). The retroviral genome may comprise other un-translated sequences, besides those mentioned above, including a primer binding site, adjacent to the U5 region, at which point the tRNA contained within the retroviral particle binds to the retroviral genome to initiate reverse transcription after infection of a host (see Coffin, above). The retroviral genome may also comprise a leader sequence between the 5′ LTR and the internal translated region. In addition, the retroviral genome may comprise a polypurine tract immediately 5′ to the U3 region.

“Retroviral vectors” as used herein also refers to vectors used to introduce into a host the cDNA nucleic acids of the present invention in the form of an RNA viral particle, as is generally outlined in PCT US 97/01019 and PCT US 97/01048, both of which are incorporated by reference. Various retroviral vectors are known, including a vector based on the murine stem cell virus (MSCV) (see Hawley, R. G. et al. (1994) Gene Ther. 1: 136-38), modified MFG virus (Riviere, I. et al. (1995) Genetics 92: 6733-37), pBABE (see PCT US97/01019), and pCRU5 (Naviaus, R. K. et al. (1996) J. Virol. 70: 5701-05), all of which are incorporated by reference. In addition, particularly well suited retroviral transfection systems for generating retroviral vectors are described in Mann et al., supra; Pear, W. S. et al. (1993) Pro. Natl. Acad. Sci. USA 90: 8392-96; Kitamura, T. et al. (1995) Proc. Natl. Acad. Sci. USA 92: 9146-50; Kinsella, T. M. et al. (1996) Hum. Gene Ther. 7: 1405-13; Hofmann, A. et al. (1996) Proc. Natl: Acad. Sci. USA 93: 5185-90; Choate, K. A. et al. (1996) Hum. Gene Ther. 7: 2247-53; WO 94/19478; PCT US97/01019, and references cited therein, all of which are incorporated by reference.

In the preferred embodiment, the retroviral vectors are self-inactivating retroviral vectors or SIN vectors. By “self-inactivating, or “SIN” or grammatical equivalents herein is meant retroviral vectors in which the viral promoter elements are rendered ineffective or inactive (see Yu, S.-F. et al. (1986) Proc. Natl. Acad. Sci. USA 83: 3094-84). These promoter and enhancer elements are present in the 3′ long terminal repeat (3′ LTR), which is composed of segments designated as U3 and R (see Fields, B. N. et al. Virology, Vol. 2, Lippincoft-Raven Publishers, New York, N.Y., 1996, pg 1767-1847). The integrated retroviral genome, called the provirus, is bound by two LTRs and is transcribed from the 5′ LTR to the 3′ LTR. The viral promoters and enhancers reside primarily in the U3 region of the 3′ LTR, but the 3′ LTR region is duplicated at the 5′ LTR during viral replication and integration. The promoter situated at the 5′ LTR directs expression of virally encoded genes and generates the RNA copies that are packaged into viral particles.

The self-activating feature of SIN vectors arises from the mechanism of viral replication and integration (see Coffin, J. M. “Retroviridae: The Viruses and Their Replication” in Virology: Vol 2, Fields et al., ed., Lippincott-Raven Publishers, New York, pg 1767-1847). Following entry of the retrovirus into a cell, a tRNA molecule binds to the primer binding region (PB) at the 5′ end of the viral RNA. Extension of the tRNA primer by reverse transcriptase results in a tRNA linked to a DNA segment containing the U5 and R sequences present at the 5′ end of the viral RNA. RNase activity of reverse transcriptase acts on the viral RNA strand of the DNA/RNA hybrid, thus releasing the elongated tRNA, which then hybridizes to complementary R sequences present on the 3′ end of the viral RNA. Elongation by reverse transcriptase results in synthesis of a DNA copy of the viral genome (minus strand DNA) and degradation of the RNA strand by RNase. A short RNA sequence designated the PP sequence, which is resistant to RNase action, remains hybridized to the newly synthesized DNA strand—generally at a region immediately preceding the U3 region at the 3′ end of the viral genome—and acts as a primer for replication of the complementary strand (plus strand DNA). Extension of this PP primer results in replication of sequences comprising U3, R, U5, and PB segments, which eventually becomes the 5′ LTR of the integrated virus. Subsequently, the PB region of the extended primer hybridizes to the complementary PB region present on the 3′ end of the minus strand DNA, and subsequent extension of this hybrid results in synthesis of a double strand DNA intermediate in which the 5′ and 3′ LTR contain the U3, R, and U5 segments. Following replication and transport into the nucleus, the viral double stranded DNA integrates into the host chromosome via the attachment sites (att) present near the ends of the LTRs to generate the integrated provirus.

Since the mechanism of viral replication results in duplication of the promoter elements at the 3′ LTR to the 5′ LTR of the integrated virus, inactivating or replacing the viral promoter results in inactivating or replacing the promoter normally present in the proviral 5′ LTR. This feature describes the self-inactivating nature of these retroviral vectors. Inactivation of the 5′ LTR promoter reduces expression of the proviral nucleic acid from the 5′ LTR and reduces the potential deleterious effects arising from influences on cellular genes by the viral promoter present on the 3′ LTR of the integrated virus.

“Retroviral vector” as used herein also refers to plasmid-based expression vectors comprising requisite cis-elements of a retroviral genome, including transcriptional and translational regulatory sequences, and packaging sequences, or functional variants thereof, which are required for the production of retroviral particles and packaging of vector into particles. By requisite cis-elements is meant those elements which are necessary for packaging the plasmid-based expression vector as a retroviral genome in a retroviral particle, and which are not supplied by other means, for example in trans by a host cell, as described below.

As used herein, retroviral vector also refers to retroviral particles comprising: a) a retroviral genome which is other than naturally occurring; or b) a plasmid-based retroviral expression vector as described above.

Preferred particles are not capable of replication after infection of a host cell which is other than a host cell that provides essential retroviral factors in trans for synthesizing and packaging retrovirus (for example, known packaging cell lines). Thus, these particles are typically capable of a single infection.

A retroviral expression vector system is generally described in PCT/US97/01019 and PCT/US97/01048, both of which are expressly incorporated herein by reference.

In one aspect, the present invention provides methods for producing retroviral cDNA expression vector libraries, which include retroviral particles.

The use of recombinant retroviruses was pioneered by Richard Mulligan and David Baltimore with the Psi-2 lines and analogous retrovirus packaging systems, based on NIH 3T3 cells (see Mann et al., Cell 33:153-159 (1993), hereby incorporated by reference). Such helper-defective packaging lines are capable of producing all the necessary trans proteins -gag, pol, and env- that are required for packaging, processing, reverse transcription, and integration of recombinant genomes. Those RNA molecules that have in cis the ψ packaging signal are packaged into maturing virions. Retroviruses are preferred for a number of reasons. First, their derivation is easy. Second, unlike Adenovirus-mediated gene delivery, expression from retroviruses is long-term (adenoviruses do not integrate). Adeno-associated viruses have limited space for genes and regulatory units and there is some controversy as to their ability to integrate. Retroviruses therefore offer the best current compromise in terms of long-term expression, genomic flexibility, and stable integration, among other features. The main advantage of retroviruses is that their integration into the host genome allows for their stable transmission through cell division. This ensures that in cell types which undergo multiple independent maturation steps, such as hematopoietic cell progression, the retrovirus construct will remain resident and continue to express.

A particularly well suited retroviral transfection system is described in Mann et al., supra: Pear et al., PNAS USA 90(18):8392-6 (1993); Kitamura et al., PNAS USA 92:9146-9150 (1995); Kinsella et al., Human Gene Therapy 7:1405-1413; Hofmann et al., PNAS USA 93:5185-5190; Choate et al., Human Gene Therapy 7:2247 (1996); and WO 94/19478; and references cited therein, all of which are incorporated by reference.

In one embodiment of the invention, the library is generated in a retrovirus DNA construct backbone. Description of an appropriate retroviral DNA construct backbone is found in Lorens et. al., Mol. Therapy, 1:438-447, 2000, incorporated herein by reference.

Any number of suitable retroviral vectors may be used. Generally, the retroviral vectors include a second nucleic acid encoding a detectable protein moiety or selection gene. Retroviral vectors may also include separation linkers such as an IRES, type 2a sequence, or cleavage site encoding sequence, as described herein. Retroviral vectors may also include promoters driving expression of a second gene, placed in sense or anti-sense relative to the 5′ LTR. Suitable selection genes include, but are not limited to, neomycin, blastocidin, bleomycin, puromycin, and hygromycin resistance genes, as well as self-fluorescent markers such as green fluorescent protein, enzymatic markers such as lacZ, and surface proteins such as CD8, etc. In a preferred embodiment, the second nucleic acid encodes a GFP from Aequorea, Renilla, or Ptilosarcus species, as described herein.

Preferred vectors include a vector based on the murine stem cell virus (MSCV) (see Hawley et al., Gene Therapy 1:136 (1994)) and a modified MFG virus (Rivere et al., Genetics 92:6733 (1995)), and pBABE, (see Moregenstern et. al., Nuc. Acids Res. 18:3587-3596, 1990; Nolan et. al., U.S. Pat. No. 6,153,380 issued Nov. 28, 2000; Hofmann et. al., Proc. Nat'l. Acad. Sci., 93:51855190, 1996; all expressly incorporated herein by reference. Another preferred vector is based on the murine leukemia. virus (for example, see Lorens et. al., Mol. Therapy, 1:438-447, 2000).

The retroviruses may include inducible and constitutive promoters. Inducible expression may be desired, for example to provide for turning peptide or antisense nucleic acid expression on and off during the selection process to confirm the effect of candidate agent or to ensure the survival of producer cells in which prolonged candidate agent expression may be lethal.

In addition, it is possible to configure a retroviral vector to allow inducible expression of retroviral inserts after integration of a single vector in target cells; importantly, the entire system is contained within the single retrovirus. Tet-inducible retroviruses have been designed incorporating the Self-Inactivating (SIN) feature of 3′ LTR enhancer/promoter retroviral deletion mutant (Hoffman et al., PNAS USA 93:5185 (1996)). Expression of this vector in cells is virtually undetectable in the presence of tetracycline or other active analogs. However, in the absence of Tet, expression is turned on to maximum within 48 hours after induction, with uniform increased expression of the whole population of cells that harbor the inducible retrovirus, indicating that expression is regulated uniformly within the infected cell population. A similar, related system uses a mutated Tet DNA-binding domain such that it bound DNA in the presence of Tet, and was removed in the absence of Tet. Either of these systems is suitable.

A preferred inducible promoter for use in the present invention is a tet-inducible promoter comprising multiple copies of the tet operon operably linked to a minimal human CMV promoter (for example, see Gossen et al., PNAS 89:5547-5551, 1992).

Delivery of the retroviral cDNA expression vectors, described herein, into a retroviral packaging system results in conversion to infectious virus. Suitable retroviral packaging system cell lines include, but are not limited to, the Bing and BOSC23 cell lines described in WO 94/19478; Soneoka et al., Nucleic Acid Res. 23(4):628 (1995); Finer et al., Blood 83:43 (1994); Pheonix packaging lines such as PhiNX-eco and PhiNX-ampho, described below; 292T+gag-pol and retrovirus envelope; PA317; and cell lines outlined in Markowitz et al., Virology 167:400 (1988), Markowitz et al., J. Virol. 62:1120 (1988), Li et al., PNAS USA 93:11658 (1996), Kinsella et al., Human Gene Therapy 7:1405 (1996), all of which are incorporated by reference.

Preferred systems include PhiNX-eco and PhiNX-ampho or similar cell lines, which are two cells lines as follows. The cell lines are based on the BING and BOSC23 cell lines described in WO 94/19478, which are based on the 293T cell line (a human-embryonic kidney line transformed with adenovirus E1a and carrying a temperature sensitive T antigen co-selected with neomycin). The unique feature of this cell line is that it is highly transfectable with either calcium phosphate mediated transfection or lipid-based transfection protocols—greater than 50% of 293T cells can be transiently transfected with plasmid DNA. Thus, the cell line is a cellular milieu in which retroviral structural proteins and genomic viral RNA can be brought together rapidly for creation of helper-defective virus. 293T cells were therefore engineered with stably integrated defective constructs capable of producing gag-pol, and envelope protein for either ecotropic or amphotropic viruses. These lines were called BOSC23 and Bing, respectively. The utility of these lines was that one could produce small amounts of recombinant virus transiently for use in small-scale experimentation. The lines offered advantages over previous stable systems in that virus could be produced in days rather than months.

Two problems became apparent with these first generation lines over the first two years they were in wide use. First, gag-pol and envelope expression was unstable and the lines required vigilant checking for retroviral production capacity; second the structure of the vectors used for protein production were not considered fully “safe” for helper virus production; and third, one of the lines was shown to be inadvertently carrying a hygromycin-containing retrovirus. Although the BING and BOSC23 lines are useful in the present invention, all of these potentially problematic issues are addressed in the PhiNX second-generation lines. These lines are based on 293T cells as well, with the following improvements. First, the ability to monitor gag-pol production on a cell-by cell basis was made by introducing an IRES-CD8 surface marker expression cassette downstream of the reading frame of the gag-pol construct (other surface markers besides CD8 are also useful). IRES (internal ribosome entry site) sequences allow secondary or tertiary protein translation from a single mRNA transcript. Thus, CD8 expression is a direct reflection of intracellular gag-pol and the stability of the producer cell population's ability to produce gag-pol can be readily monitored by flow cytometry. Second, for both the gag-pol and envelope constructs hon-Moloney promoters were used to minimize recombination potential with introduced retroviral constructs, and different promoters for gag-pol and envelope were used to minimize their inter-recombination potential. The promoters used were CMV and RSV. Two cell lines were created, PHEONIX-ECO and PHEONIX-AMPHO. Gag-pol was introduced with hygromycin as the co-selectable marker and the envelope proteins were introduced with diphtheria resistance as the co-selectable marker. Finally, the cells were screened to find a relatively rare cell type that produced gag-pol and env in a uniform distribution, although this is not required. In addition, a line termed PHEONIX-gp has been produced that expresses only gag-pol. This line is available for further pseudotyping of retroviral virions with other envelope proteins such as gibbon ape leukemia virus envelope or Vesicular Stomatitus VSV-G protein, Xenotropic, or retargeting envelopes can also be added.

Both PHEONIX-ECO and PHEONIX-AMPHO were tested for helper virus production and established as being helper-virus free. Both lines can carry episomes for the creation of stable cell lines which can be used to produce retrovirus. Both lines are readily testable by flow cytometry for stability of gag-pol (CD8) and envelope expression; after several months of testing the lines appear stable, and do not demonstrate loss of titre as did the first-generation lines BOSC23 and Bing (partly due to the choice of promoters driving expression of gag-pol and envelope). Both lines can also be used to transiently produce virus in a few days. Thus, these new lines are fully compatible with transient, episomal stable, and library generation for retroviral gene transfer experiments. Finally, the titres produced by these lines have been tested. Using standard polybrene-enhanced retroviral infection, titres approaching or above 10⁷ per ml were observed for both PHEONIX-eco and PHEONIX-ampho when carrying episomal constructs. When transiently produced virus is made, titres are usually ½ to ⅓ that value.

These lines are helper-virus free, carry episomes for long-term stable production of retrovirus, stably produce gag-pol and env, and do not demonstrate loss of viral titre over time. In addition, PhiNX-eco and PhiNX-ampho are capable of producing titres approaching or above 10⁷ per ml when carrying episomal constructs, which, with concentration of virus, can be enhanced to 10⁸ to 10⁹ per ml.

In a preferred embodiment, the cell lines disclosed above, and the other methods for producing retrovirus, are useful for production of virus by transient transfection. The virus can either be used directly or be used to infect another retroviral producer cell line for “expansion” of the library.

Concentration of virus may be done as follows. Generally, retroviruses are titred by applying retrovirus-containing supernatant onto indicator cells, such as NIH3T3 cells, and then measuring the percentage of cells expressing phenotypic consequences of infection. The concentration of the virus is determined by multiplying the percentage of cells infected by the dilution factor involved, and taking into account the number of target cells available to obtain a relative titre. If the retrovirus contains a reporter gene, such as lacZ, then infection, integration, and expression of the recombinant virus is measured by histological staining for lacZ expression or by flow cytometry (FACS). In general, retroviral titres generated from even the best of the producer cells do not exceed 10⁷ per ml, unless concentration by relatively expensive or exotic apparatus is done. However, as it has been recently postulated that since a particle as large as a retrovirus will not move very far by brownian motion in liquid, fluid dynamics predicts that much of the virus never comes in contact with the cells to initiate the infection process. However, if cells are grown or placed on a porous filter and retrovirus is allowed to move past cells by gradual gravitometric flow, a high concentration of virus around cells can be effectively maintained at all times. Thus, up to a ten-fold higher infectivity by infecting cells on a porous membrane and allowing retrovirus supernatant to flow past them has been seen. This should allow titres of 10⁹ after concentration.

The retroviral cDNA expression vector libraries provided herein each comprise three types of vectors.

In the first vector type, cDNA is operably linked to a transcriptional regulatory sequence in sense configuration. By convention, mRNA is a sense strand. Therefore, operably linked to a transcriptional regulatory sequence in sense configuration means that an antisense strand (first cDNA strand) serves as template for transcription. Additionally, in the first vector type, the cDNA is in frame relative to the normal open reading frame (ORF). That is, the cDNA fragment is linked to a translational regulatory sequence, such that a vector transcription product comprises an ORF comprising a cDNA encoded. nucleic acid sequence that will be translated in the same frame as the ORF of the corresponding mRNA used as template for cDNA synthesis. This ORF is sometimes referred to herein as the native ORF. Such a retroviral vector may be used to express a polypeptide encoded by the corresponding mRNA template used in cDNA synthesis.

A preferred inducible promoter for use in the present invention is a tet-inducible promoter comprising multiple copies of the tet operon operably linked to a minimal human CMV promoter (for example, see Gossen et al., PNAS 89: 5547-5551, 1992).

Another preferred transcriptional regulatory sequence comprises a composite CMV promoter fused to the transcriptional start site of the MMLV R-U5 region of the LTR. For example, see Lorens et. al., Mol. Therapy, 1:438-447, 2000.

In the second expression vector type, the cDNA is operably linked to a transcriptional regulatory sequence in sense configuration (i.e., antisense sequence serving as template for transcription) but translation is out of frame relative to the normal open reading frame. That is, the cDNA fragment is linked to a translational regulatory sequence such that a vector transcription product comprises an ORF comprising a cDNA encoded nucleic acid sequence that will be translated in a different frame than that of the ORF of the corresponding mRNA used as template for cDNA synthesis. Such a retroviral vector may be used to express a random polypeptide if translation is not interrupted by a stop codon in the shifted reading frame.

In the third expression vector type, the cDNA is operably linked to a transcriptional regulatory region in antisense configuration (i.e. sense sequence serving as template for transcription). Such a retroviral vector may be used to express antisense nucleic acid. In addition, antisense nucleic acid may be translated as directed by a translation start site provided. The translated peptide product will obviously not correspond to the ORF of the corresponding mRNA used to prime cDNA synthesis, and is referred to herein as a random peptide product.

Some cDNA inserts of the present expression vectors may also include nucleic acid sequence corresponding to untranslated mRNA sequence. These sequences may also be translated in the context of the present expression vectors. In addition, some vectors may harbor a native translation start site provided by the cDNA. As such, some vectors may comprise more than one translation start site.

Importantly, while a cDNA may be in sense configuration (equivalently referred to herein as sense orientation) and in frame or out of frame relative to a native ORF, or in antisense configuration (equivalently referred to herein as antisense orientation), knowledge of the positioning of cDNA in individual vectors is not required in order to use the retroviral cDNA expression vectors provided herein to deliver and express genetic effectors in cells. Accordingly, the methods provided herein involving the use of retroviral cDNA expression vector libraries to screen for cDNA-encoded bioactive agents having desired effects on a cell, do not require knowledge of the orientation and positioning of cDNAs in the vectors used. Once a genetic effector (cDNA in context of expression vector) with desired properties is identified in the functional screens described herein, the orientation and frame of the cDNA may be determined if desired.

If desired, a retroviral cDNA expression vector may be isolated and the ORF sequence determined and compared to sequences in a database of compiled nucleic acid sequences, for example the National Center for Biotechnology Information databases (Genbank) and the Celeram™ sequence databases (Applera Corporabon), to determine if the cDNA ORF, as read in the context of the vector, is in frame or out of frame with respect to a native ORF.

Alternatively, if desired, the cDNA of the vector may be used to screen a cDNA library to obtain a clone with a complete 5′ end, capturing the native translation start site and revealing the native ORF. Such methods are well known in the art (See, for example, Ausubel et al., supra; Sambrook et al., supra).

In a preferred embodiment, retroviral cDNA expression vectors provided herein comprise cDNA fragments as described herein.

An important feature of the present retroviral cDNA expression vector libraries is that they provide for the expression in a cell of a protein corresponding to a fragment of a host cell protein. This may be achieved by using mRNA isolated from a host cell to generate cDNAs, and generating cDNA fragments from these cDNAs.

A protein encoded by a cDNA fragment may comprise a segment of a native mRNA ORF and encode a fragment of a host cell protein. Such a cDNA-encoded protein fragment is predicted to possess certain activities of the host cell protein due to shared sequence, and to lack other activities of the host cell protein due to sequences that are lacking in the retroviral vector expression product as compared to the host cell protein. Importantly, such retroviral vector expression products may exhibit dominant negative activity by virtue of having a partial complement of host cell protein activities. Particularly, such retroviral vector expression products may inhibit at least one activity possessed by the corresponding host cell protein.

Alternatively, mRNA for cDNA synthesis may be derived from sources other than the host cell in Which the cDNA is to be expressed.

A cDNA-encoded protein fragment may possess unique activities and exert unique biological effects compared to molecules encoded by its corresponding mRNA (Lorens et. al., Mol. Therapy, 1:438-447, 2000). The ability to express protein microdomains can be a powerful means to subtly perturb cellular physiology in manners that reveal new paths for therapeutic intervention.

In a preferred embodiment, the retroviral expression vector library comprises a plurality of retroviral expression vectors, each vector comprising a) a first nucleic acid comprising a cDNA; b) a second nucleic acid which encodes a fusion partner; and c) a transcriptional regulatory sequence (sometimes referred to herein as a transcriptional regulatory region) recognized by a host cell. The first and second nucleic acids form a fusion nucleic acid which is operably linked to the transcriptional regulatory sequence. The vectors additionally comprise a translational regulatory sequence that initiates translation of the fusion nucleic acid.

In a preferred embodiment, the fusion partner is a detectable protein (sometimes referred to herein as detectable protein moiety or detection gene). Preferred detectable proteins are fluorescent proteins and their variants, including A. victoria GFP, Renilla mulleris GFP, Renilla reniformis GFP, Ptilosarcus gumeyi GFP, YFP, BFP and RFP.

In a preferred embodiment, the cDNA is a cDNA fragment, preferably a restriction fragment.

In one embodiment, the first nucleic acid is fused to the 5′ end of the second nucleic acid. The expression products of such a library of vectors include fusion nucleic acids wherein cDNA encoded sequence is located at the 5′ end and nucleic acid sequence encoding a detectable protein moiety is located at the 3′ end.

The expression products of such a library of vectors also include fusion proteins if translation is not interrupted by a stop codon in the cDNA fragment or at the fragment/vector ligation site. Care is taken in vector design to avoid such ligation sites. Such fusion proteins comprise N-terminal polypeptides encoded by cDNA fragments and C-terminal polypeptides which are detectable protein moieties.

The expression products of such a library of vectors also include fusion nucleic acids wherein antisense nucleic acid is located at the 5′ end and nucleic acid sequence encoding detectable protein is located at the 3′ end. Additionally, the expression products include fusion proteins comprising N-terminal polypeptides encoded by cDNA antisense transcripts and C-terminal polypeptides which are detectable protein moieties.

It will be appreciated that such an antisense nucleic acid may be used to inhibit the normal RNA processing/editing and/or translation of a host cell mRNA, particularly the template mRNA used for cDNA synthesis and mRNAs related thereto by sequence. Importantly, an advantage of such fusion antisense nucleic acids is the stability conferred to the fusion nucleic acid by inclusion of the second nucleic acid sequence which encodes a detectable protein moiety. A fusion nucleic acid of this sort in general provides an antisense nucleic acid that is more stable than antisense nucleic acid alone and is potentially more potent as an inhibitor of native mRNA processing/editing and/or translation.

When located 5′ of the nucleic acid sequence encoding the detectable protein, the cDNA fragment is cloned into the 5′ position downstream of a transcription start site and a translation start site which places the cDNA fragment in frame or out of frame with respect to the normal open reading frame of the corresponding mRNA used to prime cDNA synthesis.

In another embodiment, the expression vector does not comprise a translation start site and translation of cDNA encoded transcript relies on the occurrence of a native translation start site in the cDNA transcript.

In an especially preferred embodiment, the first nucleic acid is fused to the 3′ end of the second nucleic acid. The expression products of such a library of expression vectors include fusion nucleic acids wherein cDNA encoded sequence is located at the 3′ end and nucleic acid sequence encoding detectable protein is located at the 5′ end.

The expression products of such a library of expression vectors also include fusion proteins if translation is not interrupted by a stop codon in the cDNA fragment or at the fragment/vector ligation site. Such fusion proteins comprise C-terminal polypeptides encoded by cDNA fragments and N-terminal polypeptides which are detectable protein moieties. Termination of translation of these fusion proteins is ensured but the inclusion of a triple frame translation stop sequence cassette in the vector, downstream of the cDNA insert.

The expression products of such a library of expression vectors also include fusion nucleic acids wherein antisense nucleic acid is located at the 3′ end and nucleic acid sequence encoding detectable protein is located at the 5′ end. Importantly, an advantage of such fusion antisense nucleic acids is the stability conferred to the fusion nucleic acid by inclusion of the second nucleic acid sequence which encodes a detectable protein moiety. A fusion nucleic acid of this sort in general provides an antisense nucleic acid that is more stable than antisense nucleic acid alone and is potentially more potent as an inhibitor of native mRNA processing/editing and/or translation. Additionally, the expression products include fusion proteins comprising C-terminal polypeptides encoded by cDNA antisense transcripts and N-terminal polypeptides which are detectable protein moieties.

When located 3′ of the nucleic acid sequence encoding-detectable protein, the transcription start site and translation start site are positioned to initiate transcription and translation of the detectable protein sequence in frame, and attached cDNA sequence may be translated in frame, out of frame, or in reverse direction (antisense) depending on its position and orientation relative to the start codon upstream.

In an especially preferred embodiment, the expression vector additionally comprises a third nucleic acid sequence which is a linker, as described herein, interposed between the first and second nucleic acids.

In a preferred embodiment, the linker encodes a protein tether between cDNA-encoded protein and detectable protein moieties, as described herein.

In another embodiment, the linker is a separation sequence as described herein.

When the linker encodes a protein tether, the fusion protein expression products of the library comprise a protein tether that separates the cDNA-encoded polypeptide from the detectable protein moiety in the fusion protein. The tether sequence may be desirable to allow the cDNA-encoded polypeptide to interact with potential targets unhindered.

Particularly preferred linker sequences are MDELYKEEMKAGGSGGSSVVVR and MDELYKEEAAKAGGSGGSSVLGSA. In a preferred embodiment, a C-terminal portion of the linker sequence, of about 4 to about 5 amino acids, is encoded by adaptors which are cloned into the expression vector with cDNA.

In a preferred embodiment, the first nucleic acid is fused to the 3′ end of the second nucleic acid through a linker encoding a peptide tether. In another embodiment, the first nucleic acid is fused to the 5′ end of the second nucleic acid through a linker encoding a peptide tether.

In some embodiments, the first nucleic acid is fused to the second nucleic acid through a linker which is a separation sequence. In one embodiment, the first nucleic acid is fused to the 5′ end of the second nucleic acid through a linker. In one embodiment, the first nucleic acid is fused to the 3′ end of the second nucleic acid through a linker.

In one embodiment, the linker connecting the first and second nucleic acids comprises an internal ribosome entry sequence (IRES). IRES sequences are well known in the art, for example see Jackson et. al., Trends in Biochem. Sci., 15:477-483, 1990. Such a linker may be used to fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid and two separate polypeptides translated from a fusion nucleic acid, particularly a first polypeptide which is encoded by a cDNA fragment, and a second polypeptide which is a detectable protein. Expression of the cDNA encoded polypeptide is dependent on the absence of a stop translation codon in the cDNA fragment (or introduced at ligation sites by insertion) as read in the context of the vector.

In the case of the use of an IRES sequence, the cDNA portion of the construct is preferably upstream of the IRES, as it is well documented that the ratio of expression product upstream:downstream can reach levels as high a 10:1. By using this orientation, more of the expression product is made. The orientation matters less in the case where a 2a sequence is used.

IRES sequences provide for CAP (here used to refer to 7-methyl-Gppp cap) independent initiation of translation (Kim, et al. (1992) Mol. Cell. Biol. 12:3636-3643; McBratney, et al. (1993) Current Opinion in Cell Biology 5:961-65) and appear to act by recruiting 40S ribosomal subunit to the mRNA in the absence of translation initiation factors required for normal CAP dependent translation initiation. IRES sequences are heterogenous in nucleotide sequence, RNA structure, and factor requirements for ribosome binding and are frequently located on the untranslated leader regions of RNA viruses, such as the Picomaviruses. The viral sequences range from about 450-500 nucleotides in length, although IRES sequences may also be shorter or longer (Adam, et al. J. Virol. (1991) 65, 4985-4990; Borman et al. (1997) Nucleic Adds Res 25:925-32; Hellen, et al. (1995) Curr. Top. Microbiol. Immunol. 203: 39-63 Mounfford, et al. (1995) Trends Genet. 11: 179-184). One embodiment of the IRES separation sites are the Type I IRESs present in enteroviral and rhinoviral sequences. These sequences are not efficient initiators of translations. A more preferred embodiment of IRESs are Type II sequences of cardioviruses and aphtoviruses (i e. encephalomyocarditis virus, see Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA, 86: 6126-30.), which are efficient initiators of translation. Another embodiment are Type lIl IRES sequences, such as those found in hepatitis A viruses. Also useful in the present invention include IRES sequences found in other viruses: avian reticuloendotheleliosis virus (Lopez-Lastra, et al. (1997) Hum. Gene Ther. 8: 1855-65), Moloney murine leukemia virus (Vagner et al., (1995) J. Biol. Chem. 270: 20376-83), short IRES segments of hepatitis C virus (Urabe, et al. (1997) Gene 200: 157-62), coronavirus (Lie et al. (1991) Virology 184: 531-44), and other virus families such as flaviruses and DNA viruses (i.e. Karposi's Sarcoma-associated virus).

Additionally, preferred embodiments of IRES sequences are non-viral IRES elements found in a variety of organisms including yeast, Drosophila, birds and mammals. Like the viral IRES sequences, cellular IRES sequences are heterogeneous m sequence and secondary structure. Cellular IRES sequences, however, may comprise much shorter sequences (Oh et al. (1992) Genes Dev. 6: 1643-53; Chappell et al. (2000) 97: 1536-41). Specific IRES sequences include, but are not limited to, immunoglobulin heavy chain binding protein, transcription factors, protein kinases, protein phosphatases, eIF4G (Johannes et al. 1999; Johannes et al. 1998), vacular endothelial growth factor (Huez, et al. (1989) Mol. Cell. Biol. 18: 6178-90), c-myc (Stoneley et al. (2000) Nucleic Acids Res. 28: 87-94), pro-apoptotic protein Apaf-1 (Coldwell et al. (2000) Oncogene, 19: 899-905), DAP-5 (Henis-Korenblit et al. (2000) Molecular Cell Bio. 20: 496-506), connexin (Werner, R. (2000) IUBMB Life, 50: 173-176), Notch 2 (Lauring et al. (2000) Mol Cell. 6: 939-45), and fibroblast growth factor (Creancier, et al. (2000) J. Cell. Biol. 150: 275-281). As some IRES sequences act or function efficiently in particular cell types, the person skilled in the art will choose IRES elements with relevance to particular cells that will be expressing the retroviral cDNA expression vector. Moreover, multiple IRES sequences in various combinations, either homomultimeric or heteromultimeric, as direct tandem repeats or with linkers, are useful for increasing efficiency of translation initiation of cDNA and fusion partner. The combinations of IRES elements comprise at least 2 to 10 or more copies or combinations of IRES sequences, depending on the efficiency of initiation desired.

The present invention further contemplates use of enhancers of IRES mediated initiation sequences. IRES initiated translation may be enhanced by any number of methods. Cellular expression of virally encoded protease, which cleaves eIF4F to dissociate CAP-binding activity of the eIF4F complex from the 40S ribosome complexes, may be employed to increase preference for IRES translation initiation events. These proteases are found in certain Picornaviruses and can be expressed in a cell by introducing the viral protease gene by transfection of nucleic acids encoding the protease or introduction into the cell through retroviral delivery. Other enhancers of IRES elements that may be used with the present embodiment include cis acting elements, such as 3′ untranslated region of hepatitis C virus (Ito et al. (1998) J. Virol. 72: 8789-8786) and polyA segments (Bergamini, et al. (2000) RNA 6: 1781-1790). In addition, preferential use of cellular IRES sequences may occur when CAP dependent mechanisms are impaired, for example by dephosphorylabon of 4E-BP, proteolytic cleavage of eIF4G, or especially when cells are placed under stress such g-irradiation, amino acid starvation, or hypoxia. Thus In addition to the methods described above, activation or introduction of phosphatases acting on 4E-BP, proteases of eIF4G, or treatment to induce stress in the cell are all included in the enhancing methods. Other enhancers are trans-acting IRES factors, which include, but not limited to, heterogeneous nuclear ribonucleoprotein (hnRNP) (Kaminski et al. (1998) RNA 4: 626-638), PTB hnRNP E2/PCBP2 (Walter et al. (1999) RNA 5: 1570-1585), La autoantgen (Meerovitch et al (1993) J. Virol. 67: 3798-3807), unr (Hunt et al. (1999) Genes Dev. 13: 437-448), ITAF45/Mpp1 (Pilipenko et al (2000) Genes Dev. 14: 2028-2045), DAP5/NAT1/p97 (Henis-Korenblit et al (2000) Mol. Cell. Biol. 20: 496-506), and nucleolin (Izumi et al. (2001) Virus Res. 76: 17-29). These factors may be introduced into a cell either alone or in combination to increase efficiency of translation initiation from particular IRES elements. Accordingly, various combinations of IRES elements and enhancing factors are used to effect a separation reaction.

In one embodiment, the linker connecting the first and second nucleic acids comprises a cleavage site. Such a linker may fuse the first nucleic acid to the 5′ end or the 3′ end of the second nucleic acid. The expression products of such a vector include a fusion nucleic acid, and a fusion protein wherein the cDNA-encoded polypeptide moiety and the detectable protein moiety encoded by the second nucleic add are separated by an intervening cleavage site which is a polypeptide sequence that is recognized by a protease. This site provides for cleavage of the covalent peptide linkage which links the cDNA-encoded polypeptide moiety to the detectable protein moiety in the fusion protein and for covalent separation of the two polypeptides unless otherwise covalently linked (e.g. by cysteine bridge). Many protease recognition sites are known in the art and may be used as cleavage sites in the present invention. For example see Current Protocols in Protein Science, John Wiley & Sons, Coligan et. al. eds., updated December 2001, Chapter 21, Peptidases, expressly incorporated herein by reference.

Preferred protease cleavage sites include, but are not limited to pro sequences of retroviral proteases including human immunodeficiency virus protease and sequences recognized and cleaved by trypsin (EP 578472; Takasuga et al. (1992) J. Biochem. 112: 652), proteases encoded by Picronaviruses (Ryan, et al. (1997) J. Gen. Virol. 78: 699-723), factor X_(a) (Gardella et al. (1990) J. Biol. Chem. 265:15854; WO 9006370), collagenase (J03280893; WO 9006370; Tajima et al. (1991) J. Ferment. Bioeng. 72:362), clostripain (EP 578472), subtilisin (including mutant H64A subblisin, Forsberg et al. (1991) J. Protein Chem. 10: 517), chymosin, yeast KEX2 protease (Bourbonnais et al. (1988) J. Bio. Chem. 263:15342, thrombin (Forsberg et al., supra; Abath et al. (1991) BioTechniques 10:178), Staphylococcus aureus V8 protease or similar endoproteinase-Glu-C to cleave after Glu residues (EP 578472; Ishizaki et al. (1992) Appl. Microbiol. Biotechnol. 36:483), cleavage by Nla proteainase of tobacco etch virus (Parks et al. (1994) Anal. Biochem. 216: 413), endoproteinase-Lys-C (U.S. Pat. No. 4,414,332) and endoproteinase-Asp-N, Neisseria type 2 IgA protease (Pohiner et al. (1992) Bio/Technology 10:799-804 ), soluble yeast endoproteinase yscF (EP 467839), chymotrypsin (Altman et al. (1991) Protein Eng. 4:593), enteropeptidase (WO 9006370), and lysostaphin, a polyglycine specific endoproteinase (EP 316748).

In another embodiment, the linker is a type 2a sequence.

By type 2A sequences herein is meant sequences that when translated inhibit formation of peptide linkages during the translation process. Type 2A sequences are distinguished from IRES sequences in that 2A sequences do not involve CAP independent translation initiation. Although the mechanism of action is unclear, type 2A sequences appear to act by disrupting peptide bond formation between the nascent polypeptide chain and the incoming activated tRNA^(PRO) (Donnelly et al., J. of Virology (2001) 82, 1013-1025). An advantage of type 2A separation sequences is that near stoichiometric amounts of cDNA encoded peptide and detectable protein are made as compared to IRES sequences, and Type 2A sequences do not require additional factors as compared to protease recognition sites.

The type 2a sequence of the Foot and Mouth Disease virus is especially preferred (Ryan et. al., EMBO J., 13: 928-933, 1994).

In a preferred embodiment, the retroviral cDNA fragment expression vectors are self-inactivating (SIN) vectors. Self-inactivating vectors which contain a deletion in the enhancer and promoter sequences of the 3′ LTR and transfer this sequence to the 5′ LTR are known (Yu et. al., PNAS 83:3194-3198, 1986, expressly incorporated herein by reference.

In a preferred embodiment, the retroviral cONA expression vectors comprise a fusion partner as generally described for cDNA expression vectors above, in addition to the second nucleic acid encoding a detectable protein. Preferably, the fusion partner is fused to the first nucleic acid which is a cDNA, although fusion partners may also be fused to the second nucleic acid which encodes a detectable protein, or to both the first and second nucleic acids.

In one aspect of the invention, methods for screening for a bioactive agent capable of altering the phenotype of a cell in a desirable way are provided. Importantly, the methods have the advantage of being function-based screening methods. Accordingly, no knowledge of the mechanism by which a bioactive agent works to effect a change in phenotype is required; bioactive agents are selected based on their ability to alter a cell in an observable way. Further, while a bioactive agent may modulate a signal transduction pathway to effect a change in phenotype, no knowledge of the signaling pathway or targets therein with which the bioactive agent interacts is required. Thus, the disclosed methods are an in vivo stratagem for accessing intracellular signaling mechanisms and altering cell phenotype and do not require prior knowledge of signaling pathways or their relationship to phenotype. The invention does, however, provide tools to characterize signaling pathways and identify target molecules therein that modulate cell phenotype. These target molecules may serve as lead compounds for pharmaceutical development, and may be used to characterize signaling pathways and provide additional lead compounds.

The present methods provide a significant improvement over conventional screening techniques, as they allow the rapid screening of large numbers of oligonucleotides and their corresponding expression products in a single, in vivo step. Thus, by delivering nucleic acids to cells and then screening cells, without having to collect or synthesize candidate agents in vitro, highly efficient screening is accomplished. In addition, the present methods allow screening in the absence of significant prior characterization of the cellular defect per se.

In addition, the present methods differ significantly from prior screening methods which use only random or partially random nucleic acid and amino acid sequences (for example, see U.S. Pat. No. 6,153,380 issued to Nolan et. al. Nov. 28, 2000, expressly incorporated herein by reference). In addition to random sequence nucleic acids and peptides, the present cDNA libraries provide expression products that are directed at naturally occurring mRNAs and proteins. Particularly, the present expression vector libraries are produced using. physiological sources of mRNA and consequently are, in part, directed to the inhibition of mRNA and mRNA expression products. In a preferred embodiment, the present. retroviral libraries comprise vectors which may be used to express antisense nucleic acids and dominant negative polypeptides for inhibiting the activity of host cell mRNAs and polypeptide products thereof.

The present invention provides methods of screening for bioactive agents capable of altering the phenotype of a cell in a desirable way, using, the compositions provided herein.

In one aspect of the invention, methods of screening for a bioactive agent capable of altering the phenotype of a cell in a desirable way are provided. In one embodiment, the method comprises the steps of a) introducing a retroviral cDNA expression vector library into a plurality of cells; b) screening the plurality of cells for a cell exhibiting a phenotype which is altered in a desirable way, wherein the altered phenotype is due to the expression of a cDNA. The method may also comprise any of the steps of c) isolating at least one cell exhibiting an altered phenotype; d) isolating a nucleic acid comprising the cDNA from the cell exhibiting an altered phenotype; e) identifying the bioactive agent; and f) identifying and/or isolating the molecule(s) to which the agent binds. Additionally, in some preferred embodiments, the methods involve stimulating the plurality of cells in manner known to produce a disease-like behavioral response or a phenotype of the disease process.

In a further embodiment, the method comprises the steps of a) introducing a retroviral cDNA expression vector library into a first plurality of cells; b) contacting-the first plurality of cells with a second plurality of cells; and c) screening the second plurality of cells for a cell exhibiting a phenotype which is altered in a desirable way, wherein the altered phenotype is due to contact with the first plurality of cells and expression of cDNA in the first plurality of cells. The method may also comprise any of the steps of d) isolating a cell from the first plurality of cells which is contacted with at least one cell in the second plurality of cells exhibiting an altered phenotype; e) isolating a nucleic acid comprising the cDNA from the cell isolated from the first plurality of cells; f) identifying the bioactive agent; and g) identifying and/or isolating the molecule(s) to which the agent binds.

A general description of the techniques used for these methods and examples demonstrating the use thereof are found in U.S. Pat. No. 6,153,380 issued to Nolan et. al. Nov. 28, 2000, expressly incorporated herein by reference.

By “candidate bioactive agents” or “candidate drugs” or “candidate expression products” or grammatical equivalents herein is meant the cDNA expression vector pf the present invention, or the expression products thereof, particularly the cDNA-encoded nucleic acid and peptide expression products. Candidate bioactive agents may be translation products of the cDNA expression vectors, i.e. peptides, or transcription products of the vectors, i.e. either DNA or RNA.

Candidate nucleic acids may be tested for the ability to modulate the phenotype of a cell.

By nucleic acid or “oligonucleotide” or grammatical equivalents herein is meant at least two nucleotides covalently linked together. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, as outlined below, nucleic acid analogs are included that may have alternate backbones, comprising, for example, phosphoramide (Beaucage et al.,

Tetrahedron 49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970); Sprinzl et al., Eur. J. Biochem. 81:579 (1977); Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al., Chemica Scripta 26:141 91986)), phosphorothioate (Mag et al., Nucleic Adds Res. 19:1437 (1991); and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al., J. Am. Chem. Soc. 111:2321 (1989), O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895 (1992); Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992); Nielsen, Nature, 365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which are incorporated by reference). Other analog nucleic acids include those with positive backbones (Denpcy et al., Proc. Natl. Acad. Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew. Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597 (1994); Chapters 2 and 3, ASC Symposium Series 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al., Bioorganic & Medicinal Chem. Left. 4:395 (1994); Jeffs et al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Left. 37:743 (1996)) and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook. Nucleic adds containing one or more carbocyclic sugars are also included within the definition of nucleic acids (see Jenkins et al., Chem. Soc. Rev. (1995) pp169-176). Several nucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997 page 35. All of these references are hereby expressly incorporated by reference. These modifications of the ribose-phosphate backbone may be done to increase the stability and half-life of such molecules in physiological environments.

The nucleic acids may be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequence. The nucleic acid may be DNA, both genonic and cDNA, RNA or hybrid, where the nucleic acid contains any combination of deoxyribo- and ribonucleotides, and any combination of bases, including uracil, adenine, thymine, cytosine, guanine,xanthanine hypoxanthanine, isocytosine, isoguanine, etc., although generally occurring bases are preferred. As used herein, the term “nucleoside includes nucleotides as well as nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides. In addition, “nucleoside” includes non-naturally occurring analog structures. Thus for example the individual units of a peptide nucleic add, each containing a base, are referred herein as a nucleotide.

In a preferred embodiment, the candidate bioactve agents are translation products of cDNA expression vectors. In this embodiment, the cDNA expression vectors are introduced into cells and used to express peptides. Thus, in this embodiment, the candidate bioactive agents are peptides. By “peptide”, “polypeptide”, “oligopeptide” or “protein” herein is meant at least two covalently attached amino acids. In a preferred embodiment, a protein is made up of naturally occurring amino acids and peptide bonds, such as proteins synthesized by the cellular translation system; However, as used below, a protein may also be made up of synthetic peptidomimetic structures. Thus “amino acid” or “peptide residue” as used herein means both naturally occurring and synthetic amino acids. For example, homo-phenylalanine, citrulline, and norleucine are considered amino acids for the purposes of the invention. “Amino acids” also includes imino residues such as proline and hydroxyproline. The side chains may be either the (R) or (S) configuration. In the preferred embodiment, the amino acids are in the (S) or L configuration. If non-naturally occurring side chains are used, non-amino acid substituents may be used, for example to prevent or retard in-vivo degradations. Proteins including non-naturally occurring amino acids may be synthesized or in some cases, made by recombinant techniques (see van Hest et al. (1998) FEBS Lett. 428:68-70 and Tang et al. (1999) Abstr. Pap. Am. Chem. S218: U138-U138 Part 2, both of which are expressly incorporated by reference herein).

The candidate peptides comprise a cDNA-encoded peptide moiety. The cDNA may be translated in frame, or may be translated as random peptide, as described herein. In a preferred embodiment, the candidate peptides additionally comprise a detectable protein moiety and are fusion proteins. In a preferred embodiment, the detectable protein moiety is an autofluorescent protein. In a further preferred embodiment, the autofluorescent protein is GFP, preferably GFP from Aqueora, Renilla, or Ptilosarcus species, as described herein.

It will be appreciated that a plurality of expression vectors are used to express a plurality of fusion proteins having different cDNA-encoded moieties and the same detectable protein moiety. It is understood that differences in the activities of candidate agents are due to differences in the cDNA-encoded expression products. Accordingly, the cDNA and expression products thereof are sometimes referred to herein as bioactive agents.

In a preferred embodiment, candidate bioactive agents are translation products of retroviral cDNA expression vectors.

In a preferred embodiment, candidate nucleic acids are introduced into host cells in the form of RNA genomes of retroviruses by transduction with retroviral particles, as described below.

In a preferred embodiment, the candidate bioactive agents are transcription products of the cDNA expression vectors, and are thus also nucleic acids. The candidate agents comprise a cDNA-encoded. nucleic acid. The cDNA nucleic acid may be in sense or antisense orientation. In a preferred embodiment, the candidate agents additionally comprise a nucleic acid encoding a detectable protein and are fusion nucleic acids. In a preferred embodiment, the detectable protein moiety is an autofluorescent protein. In a further preferred embodiment, the autofluorescent protein is GFP, preferably GFP from Aqueora, Renilla, or Ptilosarcus species, as described herein.

In a preferred embodiment, the candidate bioactive agents are transcription products of retroviral cDNA expression vectors. The transcription products may be either primary transcripts or secondary transcription products. That is, using the retroviral reverse transcriptase, primary DNA is made which is later converted into double stranded DNA. Additionally, using the primary DNA, RNA transcripts can be generated within the cell, including mRNA and antisense RNA.

In a preferred embodiment, the cDNA is fused to a fusion partner, as described herein.

In an especially preferred embodiment, the fusion partner is a detectable protein selected from the group consisting of GFPs from Aqueora, Renilla, or Ptilosarcus species, as described herein.

Where the fusion partner is a rescue tag, as described herein, preferably, the rescue tag is fused to the cDNA fragment encoded polypeptide moiety.

As discussed above, the cDNA may be 5′, 3′, or situated within an internal position of the fusion partner, with the appropriate location depending on the particular fusion partner, as is known in the art. In a preferred embodiment, the fusion partner is a detectable protein and cDNA encoded peptide is fused to the C-terminus of the detectable protein.

In the screening methods provided herein, generally, cDNA expression vectors are expressed within host cells to produce candidate bioactive agents. As outlined above, the candidate agents include translation products, i.e. peptides, and transcription products, i.e. nucleic acids. The cDNA expression vectors are introduced into cells to screen for bioactive agents capable of altering the phenotype of a cell in a desirable way.

By “introduced into” or grammatical equivalents herein is meant that the nucleic acids enter the cells in a manner suitable for subsequent expression of the nucleic acid. The preferred method of the present invention is transduction by retroviral particle, although other methods may be used.

Thus, in a preferred embodiment, retroviral cDNA expression vectors are used to produce retroviral particles in appropriate retroviral packaging cells as described herein. In this embodiment, a retroviral cDNA fragment expression vector is packaged in the form of a retroviral genome which may then be introduced to a host cell for expression of candidate agents including nucleic acids and polypeptides.

However, it will be recognized by those in the art that other methods of nucleic acid introduction, such as CaPO₄ precipitation, liposome fusion, lipofectin®, and electroporation, may be used. The candidate nucleic acids may stably integrate into the genome of the host cell (for example, with retroviral introduction, outlined below), or may exist either transiently or stably in the cytoplasm (i.e. through the use of traditional plasmids, utilizing standard regulatory sequences, selection markers, etc.). As many pharmaceutically important screens require human or model mammalian cell targets, retroviral vectors capable of transfecting (or transducing) such targets are preferred.

In a preferred embodiment, the candidate nucleic acids are part of a retroviral particle which infects the cells. Generally, infection of the cells is straightforward with the application of the infection-enhancing reagent polybrene, which is a polycation that facilitates viral binding to the target cell. Infection can be optimized such that each cell generally expresses a single construct, using the ratio of virus particles to number of cells. Infection follows a Poisson distribution.

In a preferred embodiment, the candidate nucleic acids are introduced into the cells using retroviral vectors. Currently, the most efficient gene transfer methodologies harness the capacity of engineered viruses, such as retroviruses, to bypass natural cellular barriers to exogenous nucleic acid uptake.

The candidate nucleic acids, as part of the retroviral construct, are introduced into the cells to screen for bioactive agents capable of altering the phenotype of a cell.

As will be appreciated by those in the art, the type of cells used in the present invention can vary widely. Basically, any mammalian cells may be used, with mouse, rat, primate and human cells being particularly preferred, although as will be appreciated by those in the art, modifications of the system by pseudotyping allows all eukaryotic cells to be used, preferably higher eukaryotes. As is more fully described below, a screen will be set up such that the cells exhibit a selectable phenotype in the presence of a bioactive agent. As is more fully described below, cell types implicated in a wide variety of disease conditions are particularly useful, so long as a suitable screen may be designed to allow the selection of cells that exhibit an altered phenotype .as a consequence of the presence of a bioactive agent within the cell.

Accordingly, suitable cell types include, but are not limited to, tumor cells of all types (particularly melanoma, myeloid leukemia, carcinomas of the lung, breast, ovaries, colon, kidney, prostate, pancreas and testes), cardiomyocytes, endothelial cells, epithelial cells, lymphocytes (T-cell and B cell), mast cells, eosinophils, vascular intimal cells, hepatocytes, leukocytes including mononuclear leukocytes, stem cells such as haemopoetic, neural, skin, lung, kidney, liver and myocyte stem cells (for use in screening for differentiation and de-differentiation factors), osteoclasts, chondrocytes and other connective tissue cells, keratinocytes, melanocytes, liver cells, kidney cells, and adipocytes. Suitable cells also include known research cells, including, but not limited to, Jurkat.T cells, NIH3T3 cells, CHO, Cos, HeLa, NIH 3T3 etc. See the ATCC cell line catalog, hereby expressly incorporated by reference. Also included are cells from the following tissue types: adipose, adrenal, adult brain, adult liver, adult ovary, amygdala, aorta, bladder, blood, bone marrow, brain tumor, breast, breast tumor, capillary endothelial cells, carcinoma, cerebellum, cervix, chondrocyte, colon, colon tumor, colorectal adenocarcinoma, embryo, embryonic brain, embryonic adrenal, embryonic eye, embryonic gut, embryonic liver, embryonic lung, embryonic muscle, embryonic spleen, endothelial, epidermis, epithelial cell, erythroleukemia, esophageal tumor, esophagus, eye, fetus, fetal brain, fetal adrenal, fetal eye, fetal gut, fetal liver, fetal lung, fetal muscle, fetal spleen, fibroblast, fibrosarcoma, glioblastoma, glioma, heart, adult heart, hepatocarcinoma, hepatoma, hippocampus, hypothalamus, intestine, small intestine, keratinocyte, kidney, kidney tumor, liver, liver tumor, lung, lung tumor, lymph node, lymphocyte, lymphoblast, lymphoma, macrophage, microglia, mammary gland, mucus-producing gland, muscle, myoblast, monocyte, nasal mucosa, neuronal, stomach, thyroid, uterus, oocyte, pancreas, ovarian tumor, pituitary, prostate, rectal tumor, rectum, retina, salivary gland, spinal cord, spleen, submucosa, stem cell, and tonsil.

In one embodiment, the cells may be genetically engineered, that is, contain exogeneous nucleic acid, for example, to contain target molecules that are exogenous.

In a preferred embodiment, a first plurality of cells is screened. That is, the cells into which the candidate nucleic acids are introduced are screened for an altered phenotype. Thus, in this embodiment, the effect of the bioactive agent is seen in the same cells in which it is made; i.e. an autocrine effect.

By a “plurality of cells” herein is meant roughly from about 10³ cells to 10⁸ or 10⁹, with from 10⁶ to 10⁸ being preferred. This plurality of cells comprises a cellular library, wherein generally each cell within the library contains a member of the retroviral molecular library, i.e. a different candidate nucleic acid, although as will be appreciated by those in the art, some cells within the library may not contain a retrovirus, and some may contain more than one. When methods other than retroviral infection are used to introduce the candidate nucleic acids into a plurality of cells, the distribution of candidate nucleic acids within the individual cell members of the cellular library may vary widely, as it is generally difficult to control the number of nucleic acids which enter a cell during electroporation, etc.

In a preferred embodiment, the candidate nucleic acids are introduced into a first plurality of cells, and the effect of the candidate bioactive agents is screened in a second or third plurality of cells, different from the first plurality of cells, i.e. generally a different cell type. That is, the effect of the bioactive agents is due to an extracellular effect on a second cell; i.e. an endocrine or paracrine effect. This is done using standard techniques. The first plurality of cells may be grown in or on one media, and the media is allowed to touch a second plurality of cells, and the effect measured. Alternatively, there may be direct contact between the cells. Thus, “contacting” is functional contact, and includes both direct and indirect. In this embodiment, the first plurality of cells may or may not be screened.

If necessary, the cells are treated to conditions suitable for the expression of the candidate nucleic acids (for example, when inducible promoters are used), to produce the candidate expression products, either translation or transcription products.

Thus, the methods of the present invention comprise introducing a molecular library of candidate nucleic acids into a plurality of cells to form a cellular library comprising candidate nucleic acids. Each of the nucleic acids comprises a cDNA. The plurality of cells is then screened, as is more fully outlined below, for a cell exhibiting an altered phenotype. The altered phenotype is due to the presence of a bioactive agent.

By “altered phenotype” or “changed physiology” or other grammatical equivalents herein is meant that the phenotype of the cell is altered in some way, preferably in some detectable and/or measurable way. As will be appreciated in the art, a strength of the present invention is the wide variety of cell types and potential phenotypic changes which may be tested using the present methods. Accordingly, any phenotypic change which may be observed, detected, or measured may be the basis of the screening methods herein. Suitable phenotypic changes include, but are not limited to: gross physical changes such as changes in cell morphology, cell growth, cell viability, adhesion to substrates or other cells, and cellular density; changes in the expression of one or more RNAs, proteins, lipids, hormones, cytokines, or other molecules; changes in the equilibrium state (i.e. half-life) or one or more RNAs, proteins, lipids, hormones, cytokines, or other molecules; changes in the localization of one or more RNAs, proteins, lipids, hormones, cytokines, or other molecules; changes in the bioactivity or specific activity of one or more RNAs, proteins, lipids, hormones, cytokines, receptors, or other molecules; changes in the secretion of ions, cytokines, hormones, growth factors, or other molecules; alterations in cellular membrane potentials, polarization, integrity or transport; changes in infectivity, susceptability, latency, adhesion, and uptake of viruses and bacterial pathogens; etc. By “capable of altering the phenotype” herein is meant that the bioactive agent can change the phenotype of the cell in some detectable and/or measurable way.

The altered phenotype may be detected in a wide variety of ways, as is described more fully below, and will generally depend and correspond to the phenotype that is being changed. Generally, the changed phenotype is detected using, for example: microscopic analysis of cell morphology; standard cell viability assays, including both increased cell death and increased cell viability, for example, cells that are now resistant to cell death via virus, bacteria, or bacterial or synthetic toxins; standard labeling assays such as fluorometric indicator assays for the presence or level of a particular cell or molecule, including FACS or other dye staining techniques; biochemical detection of the expression of target compounds after killing the cells; etc. In some cases, as is more fully described herein, the altered phenotype is detected in the cell in which the cDNA expression vector was introduced; in other embodiments, the altered phenotype is detected in a second cell which is responding to some molecular signal from the first cell as a consequence of candidate agent expression in the first cell.

In a preferred embodiment, once a cell with an altered phenotype is detected, the cell is isolated from the plurality which do not have altered phenotypes. This may be done in any number of ways, as is known in the art, and will in some instances depend on the assay or screen. Suitable isolation techniques include, but are not limited to, FACS, lysis selection using complement, cell cloning, scanning by Fluorimager, expression of a “survival” protein, induced expression of a cell surface protein or other molecule that can be rendered fluorescent or taggable for physical isolation; expression of an enzyme that changes a non-fluorescent molecule to a fluoroscent one; overgrowth against a background of no or slow growth; death of cells and isolation of DNA or other cell vitality indicator dyes, etc.

In a preferred embodiment, the candidate nucleic acid and/or the bioactive agent is isolated from the positive cell. This may be done in a number of ways in a preferred embodiment, primers complementary to DNA regions common to the retroviral constructs, or to specific components of the library such as a rescue sequence, defined above, are used to “rescue” the candidate nucleic acid. Alternatively, the bioactive agent is isolated using a rescue sequence. Thus, for example, rescue sequences comprising epitope tags or purification sequences may be used to pull out the bioactive agent, using immunoprecipitation or affinity columns. In some instances, as is outlined below, this may also pull out the primary target molecule, if there is a sufficiently strong binding interaction between the bioactve agent and the target molecule. Alternatively, the peptide may be detected using mass spectroscopy.

Once rescued, the sequence of the bioactive agent and/or bioactve nucleic acid is determined. This information can then be used in a number of ways.

In a preferred embodiment, the bioactive agent is resynthesized and reintroduced into the target cells, to verify the effect. This may be done using retroviruses, or alternatively using fusions to the HIV-1 Tat protein, and analogs and related proteins, which allows very high uptake into target cells. See for example, Fawell et al., PNAS USA 91:664 (1994); Frankel et al., Cell 55:1189 (1988); Savion et al., J. Biol. Chem. 256:1149 (1981); Derossi et al., J. Biol. Chem. 269:10444 (1994); and Baldin et al., EMBO J. 9:1511 (1990), all of which are incorporated by reference.

In a preferred embodiment, the sequence of a bioactive agent is used to generate more candidate bioactive agents. For example, the sequence of the bioactive agent may be used to develop bioactve agents with increased or altered activities through mutation. Alternatively, bioactve agents with different affinity may be sought through mutation. Furthermore, it may be desirable to put the identified cDNA-fragment expression product into other presentation structures, or to alter the sequence of the constant region of the presentation structure, to alter the conformaton/shape of the bioactive agent. It may also be desirable to “walk” around a potential binding site, in a manner similar to the mutagenesis of a binding pocket, by keeping one end of the ligand region constant and randomizing the other end to shift the binding of the peptide around.

In a preferred embodiment, either the bioactive agent or the bioactive nucleic acid encoding it is used to identify target molecules. Bioactive agents interact with target molecules to modulate or alter cell phenotype. As will be appreciated by those in the art, there may be primary target molecules, to which the bioactive agent binds or acts upon directly, and secondary target molecules, which are part of the signaling pathway affected by the bioactve agent; these might be termed “validated targets”.

In a preferred embodiment, the bioactive agent is used to pull out target molecules. For example, as outlined herein, if the target molecules are proteins, the use of epitope tags or purification sequences can allow the purification of primary target molecules via biochemical means (coammunoprecipitation, affinity columns, etc.). Altematively, the peptide, when expressed in bacteria and purified, can be used as a probe against a bacterial cDNA expression library made from mRNA of the target cell type. Or, peptides can be used as “bait” in either yeast or mammalian two or three hybrid systems. Such interaction cloning approaches have been very useful to isolate DNA-binding proteins and other interacting protein components. The peptide(s) can be combined with other pharmacologic activators to study the epistatic relationships of signal transduction pathways in question. It is also possible to synthetically prepare labeled peptide bioactive agent and use it to screen a cDNA library expressed in bacteriophage for those cDNAs which bind the peptide. Furthermore, it is also possible that one could use cDNA cloning via retroviral libraries to “complement” the effect induced by the peptide. In such a strategy, the peptide would be required to be stochiometrically titrating away some important factor for a specific signaling pathway. If this molecule or activity is replenished by over-expression of a cDNA from within a cDNA library, then one can clone the target. Similarly, cDNAs cloned by any of the above yeast or bacteriophage systems can be reintroduced to mammalian cells in this manner to confirm that they act to complement function in the system the peptide acts upon.

Once primary target molecules have been identified, secondary target molecules may be identified in the same manner, using the primary target as the “bait”. In this manner, signaling pathways may be elucidated. Similarly, bioactve agents specific for secondary target molecules may also be discovered, to allow a number of bioactve agents to act on a single pathway, for example for combination therapies.

The screening methods of the present invention may be useful to screen a large number of cell types under a wide variety of conditions. Generally, the host cells are cells that are involved in disease states, and they are tested or screened under conditions that normally result in undesirable consequences on the cells. When a suitable bioactve agent is found, the undesirable effect may be reduced or eliminated. Alternatively, normally desirable consequences may be reduced or eliminated, with an eye towards elucidating the cellular mechanisms associated with the disease state or signaling pathway.

In preferred embodiments, methods of screening for bioactve agents capable of modulating the following physiological processes or biochemical activities are provided: IgE production in B cells; mast cell activation by IgE binding; mast cell degranulation; B cell activation and antibody secretion in response to antigen receptor stimulation; T cell activation in response to antigen receptor stimulation; epithelial cell activation; E3 ubiquitin ligase activity; inflammation induced by E3 ubiquitin ligase activity; inflammation induced by TNF activity; apoptosis in activated T cells; angiogenesis; uncontrolled cell proliferation; uncontrolled cell proliferation mediated by E3 ubiquitin ligase activity; and translation of Hepatitis C-encoded proteins. Methods for measuring these activities and processes are found in U.S. patent application Ser. Nos. 10/039,761; 09/062,330; 09/293,670; 09/826,312; 09/050,861; 09/425,324; 09/076,624, each incorporated herein in their entirety by reference; and U.S. Provisional Patent Application Ser. No. 60/316,723, incorporated herein in its entirety by reference.

In one embodiment, the present invention is useful in identifying modulators of the immune response. For example, activation of B-cells initiates various facets of humoral immunity, including immunoglobulin synthesis and antigen presentation by B-cells. Activation is mediated by engagement of the B-cell receptor (BCR), for example by binding of ant-IgM F(ab′) fragments, which induces several signal transduction pathways leading to various responses by the B-cell, including immunoglobulin synthesis and secretion, apoptosis, expression of cell surface marker CD69, and modulation of IgH promoter activity. cDNA expression vector are introduced into appropriate B-cell lines, such as Ramos Human B-cell lines, M12.4 etc., to identify various effectors of the signaling pathways activated by B-cell receptor engagement. The assays may comprise determining the level of CD69 cell surface marker (i.e. by fluorescently labeled anti-CD69 antibody and FACS selection of cells expressing high levels of CD69) following receptor activation.

In a preferred embodiment, the present methods and compositions are useful for screening for agents capable of modulating exocytosis. By “alteration” or “modulation” in relation to exocytosis is meant a decrease or increase in amount or frequency of exocytosis in one cell compared to another cell or in the same cell under different conditions. Often mediated by specialized cells, exocytosis is vital for a variety of cellular processes, including neurotransmitter release by neurons, hormone release by adrenal chromaffin cells (adrenaline) and pancreatic β-cells (insulin), and histamine release by mast cells.

Disorders involving exocytosis are numerous. For example, inflammatory immune response mediated by mast cells leads to a variety of disorders, including asthma and allergies. Therapy for allergy remains limited to blocking mediators released by mast cells (i.e. anti-histamines) and non-specific anti-inflammatory agents, such as steroids and mast cell stabilizers. These treatments are only marginally effective in alleviating the symptoms of allergy. To identify cellular targets for drug design or candidate effectors of exocytosis, cDNA expression vectors may be introduced into appropriate cells, for example mast cells, and selected for modulation of exocytosis by assaying for changes in cellular exocytosis properties. These cells are stimulated with appropriate inducer if exocytosis is triggered by an inducing signal.

Assays for changes in exocytosis may comprise sorting cells in a fluorescence cell sorter (FACS) by measuring alterations of various exocytosis indicators, such as light scattering, fluorescent dye uptake, fluorescent dye release, granule release, and quantity of granule specific proteins (as provided in U.S. Ser. No. 09/293,670, incorporated herein by reference). Use of combinations of indicators reduces background and increases specificity of the sorting assay.

The exocytosis assay based on changes in the cell's light scattering properties, including use of forward and side scatter properties of the cells, are indicative of the size, shape, and granule content of the cell. Multiparameter FACS selection based on light scattering properties of cells are well known in the art, (see Perretti, M. et al. (1990) J. Pharmacol. Methods 23: 187-94; Hide, I. et al. (1993) J. Cell Biol. 123: 585-93).

Assays based on uptake of fluorescent dyes reflect the coupling of exocytosis and endocytosis in which endocytosis levels indirectly reflect exocytosis levels since the cell attempts to maintain cell volume and membrane integrity as the amount of cell membrane rapidly changes when secretory vesicles fuse with the cell membrane. Preferred fluorescent dyes include styryl dyes, such as FM1-43, FM4-64, FM14-68, FM2-10, FM4-84, FM1-84, FM14-27, FM14-29, FM3-25, FM3-14, FM5-55, RH414, FM6-55; FM10-75, FM1-81, FM9-49, FM4-95, FM4-59, FM9-40, and combinations thereof. Styryl dyes such as FM1-43 are only weakly fluorescent in water but very fluorescent when associated with a membrane, such that dye uptake by endocytosis is readily discernable (Betz, et al. (1996) Current Opinion in Neurobiology, 6:365-371; Molecular Probes, Inc., Eugene, Oreg., “Handbook of Fluorescent Probes and Research Chemicals”, 6th-Edition, 1996, particularly, Chapter 17, and more particularly, Secton 2 of Chapter 17, (including referenced related chapter), hereby incorporated herein by reference). Useful solution dye concentration is about 25 to 1000-5000 nM, with from about 50 to about 1000 nM being preferred, and from about 50 to 250 being particularly preferred.

Exocytosis assays based on fluorescent dye release rely on release of dye that is taken up passively by the cell or dye that is actively endocytosed by the cell. Release of dyes initially taken up by a cell results in decreased cellular fluorescence and presence of the dye in the cellular medium, thus providing two ways to measure dye release. For example, styryl dyes taken up into cells by endocytosis is released into the cellular media by exocytosis, resulting in decreased cellular fluorescence and presence of the dye in the medium. Another dye release assay uses low pH dyes, such as acridine orange, LYSOTRACKER™ red, LYSOTRACKER™ green,. and LYSOTRACKER™ blue (Molecular Probes, supra), which stains exocytic granules when dye is internalized by the cell.

Preferential staining of exocytic granules when the vesicles fuse with the cell membrane provides an additional assay for measuring exocytosis. Annexin V, which binds to phospholipid (phosphatidyl serine) in a divalent ion dependent manner, specifically binds to exocytic granules present on the cell surface but fails to bind internally localized exocytic granules. This property of Annexin provides a basis for determining exocytosis by the level of Annexin bound to cells. Cells show an increase in Annexin binding in proportion to the time and intensity of the exocytic response. Annexin is detectable directly by use of fluorescently labeled Annexin derivatives (i.e. FITC, TRITC, AMCA, APC, or Cy-5 fluorescent labels), or indirectly by use of Annexin modified with a primary label (e.g. biotin), which is detected using a labeled secondary agent that binds to the primary label (e.g. fluorescently labeled avidin).

Alternatively, in a preferred embodiment the exocytosis indicators are engineered into the cells. For example, recombinant proteins comprising fusion proteins of a granule specific, or a secreted protein, and a reporter molecule are expressed in a cell by transforming the cells with a fusion nucleic acid encoding a fusion protein comprising a granule specific or secreted protein and a reporter protein. This is generally done as is known in the art, and will depend on the cell type. Generally, for mammalian cells, retroviral vectors are preferred for delivery of the fusion nucleic acid. Preferred reporter molecules include, but are not limited to, Aequoria victoria GFP, Renilla mullers GFP, Renilla reniformis GFP, Renilla Ptilosarcus, GFP, BFP, YFP, and enzymes including luciferases (Renilla, firefly etc.) and β-galactosidases. Presence of the granule protein-reporter fusion construct on the cell surface or presence of secreted protein-reporter fusion construct in the medium indicates the level of exocytosis in the cells. Thus, in one preferred embodiment cells are transformed with retroviral vectors expressing a fusion protein comprising granule specific (i.e. secretory vesicle) proteins, such as VAMP (synaptobrevin) or synaptotagmin, fused to a GFP reporter molecule. The cells are monitored for localization of the fusion protein to the cell membrane. Candidate agents (cDNA expression vectors) are introduced into these transformed cells and are tested for their ability to affect distribution of the fusion protein. Since the definition of granule specific proteins encompasses mediators released during exocytosis, including, but not limited to, serotonin, histamine, heparin, hormones, etc., these granule proteins may be identified using specific antibodies.

In a preferred embodiment, the present methods are useful in cancer applications. The ability to rapidly and specifically kill tumor cells is a cornerstone of cancer chemotherapy. In general, using the methods of the present invention, cDNA expression libraries can be introduced into any tumor cell (primary or cultured), and bioactive agents identified which by themselves induce apoptosis, cell death, loss of cell division or decreased cell growth. The methods of the present invention can be combined with other cancer therapeutics (e.g. drugs or radiation) to sensitize the cells and thus induce rapid and specific apoptosis, cell death, loss of cell division or decreased cell growth after exposure to a secondary agent. Similarly, the present methods may be used in conjunction with known cancer therapeutics to screen for agonists to make the therapeutic more effective or less toxic. This is particularly preferred when the chemotherapeutic is very expensive to produce such as taxol. Known oncogenes such as v-Abl, v-Src, v-Ras, and others, induce a transformed phenotype leading to abnormal cell growth when transfected into certain cells. This is also a major problem with micro-metastases. Thus, in a preferred embodiment, non-transformed cells can be transfected with these oncogenes, and then cDNA fragment libraries introduced into these cells, to select for bioactive agents which reverse or correct the transformed state. One of the signal features of oncogene transformation of cells is the loss of contact inhibition and the ability to grow in soft-agar. When transforming viruses are constructed containing v-Abl, v-Src, or v-Ras in IRES-puro retroviral vectors, infected into target 3T3 cells, and subjected to puromycin selection, all of the 3T3 cells hyper-transform and detach from the plate. The cells may be removed by washing with fresh medium. This can serve as the basis of a screen, since cells which express a bioactive agent will remain attached to the plate and form colonies.

Similarly, the growth and/or spread of certain tumor types is enhanced by stimulatory responses from growth factors and cytokines (PDGF, EGF, Heregulin, and others) which bind to receptors on the surfaces of specific tumors. In a preferred embodiment, the methods of the invention are used to inhibit or stop tumor growth and/or spread, by finding bioactive agents capable of blocking the ability of the growth factor or cytokine to stimulate the tumor cell. The methods involve the introduction of cDNA fragment libraries into specific tumor cells with the addition of the growth factor or cytokine, followed by selection of bioactive agents which block the binding, signaling, phenotypic and/or functional responses of these tumor cells to the growth factor or cytokine in question.

Similarly, the spread of cancer cells (invasion and metastasis) is a significant problem limiting the success of cancer therapies. The ability to inhibit the invasion and/or migration of specific tumor cells would be a significant advance in the therapy of cancer. Tumor cells known to have a high metastatic potential (for example, melanoma, lung cell carcinoma, breast and ovarian carcinoma) can have cDNA expression libraries introduced into them, and peptides selected which in a migration or invasion assay, inhibit the migration and/or invasion of-Specific tumor cells. Particular applications for inhibition of the metastatic phenotype, which could allow a more specific inhibition of metastasis, include the metastasis suppressor gene NM23, which codes for a dinucleoside diphosphate kinase. Thus intracellular peptide activators of this gene could block metastasis, and a screen for its upregulation (by fusing it to a reporter gene) would be of interest. Many oncogenes also enhance metastasis. Peptides which inactivate or counteract mutated RAS oncogenes, vMOS, v-RAF, A-RAF, v-SRC, v-FES, and v-FMS would also act as anti-metastatics. Peptides, which act intracellularly to block the release of combinations of proteases required for invasion, such as the matrix metalloproteases and urokinase, could also be effective antimetastatics.

In a preferred embodiment, the cDNA fragment libraries of the present invention are introduced into tumor cells known to have inactivated tumor suppressor genes, and successful reversal by either reactivation or compensation of the knockout would be screened by restoration of the normal phenotype. A major example is the reversal of p53-inactivating mutations, which are present in 50% or more of all cancers. Since p53's actions are complex and involve its action as a transcription factor, there are probably numerous potential ways a peptide or small molecule derived from a peptide could reverse the mutation. One example would be upregulation of the immediately downstream cyclin-dependent kinase p21CIP1/WAF1. To be useful such reversal would have to work for many of the different known p53 mutations. This is currently being approached by gene therapy; one or more small molecules which do this might be preferable.

Another example involves screening for bioactive agents which restore the constitutive function of the brca-1 or brca-2 genes, and other tumor suppressor genes important in breast cancer such as the adenomatous polyposis coli gene (APC) and the homolog of the Drosophila discs-large gene (Dlg), which are components of cell-cell junctions. Mutations of brca-1 are important in hereditary ovarian and breast cancers, and screening for bioactive agents capable of suppressing these cancers is an additional application of the present invention.

In a preferred embodiment, the methods of the present invention are used to create novel cell lines from cancers from patients. A retroviral delivered candidate agents which inhibits the final common pathway of programmed cell death should allow for short- and possibly long-term cell lines to be established. Conditions of in vitro culture and infection of human leukemia cells will be established. There is a real need for methods which allow the maintenance of certain tumor cells in culture long enough to allow for physiological and pharmacological studies. Currently, some human cell lines have been established by the use of transforming agents such as Ebstein-Barr virus that considerably alters the existing physiology of the cell. On occasion, cells will grow on their own in culture but this is a random event. Programmed cell death (apoptosis) occurs via complex signaling pathways within cells that ultimately activate a final common pathway producing characteristic changes in the cell leading to a non-inflammatory destruction of the cell. It is well known that tumor cells have a high apoptotic index, or propensity to enter apoptosis in vivo When cells are placed in culture, the in vivo stimuli for malignant cell growth are removed and cells readily undergo apoptosis. The objective would be to develop the technology to establish cell lines from any number of primary tumor cells, for example primary human leukemia cells, in a reproducible manner without altering the native configuration of the signaling pathways in these cells. By introducing nucleic acids encoding peptides which inhibit apoptosis, increased cell survival in vitro, and hence the opportunity to study signaling transduction pathways in primary human tumor cells, is accomplished. In addition, these methods may be used for culturing primary cells, i.e. non-tumor cells.

In a preferred embodiment, the present methods are useful in cardiovascular applications. In a preferred embodiment, cardiomyocytes may be screened for the prevention of cell damage or death in the presence of normally injurious conditions, including, but not limited to, the presence of toxic drugs (particularly chemotherapeutic drugs), for example, to prevent heart failure following treatment with adriamycin; anoxia, for example in the setting of coronary artery occlusion; and autoimmune cellular damage by attack from activated lymphoid cells (for example as seen in post viral myocarditis and lupus). Candidate bioactive agents are inserted into cardiomyocytes, the cells are subjected to the insult, and bioactive agents are selected that prevent any or all of: apoptosis; membrane depolarization (i.e. decrease arrythmogenic potential of insult); cell swelling; or leakage of specific intracellular ions, second messengers and activating molecules (for example, arachidonic acid and/or lysophosphatidic acid).

In a preferred embodiment, the present methods are used to screen for diminished arrythmia potential in cardiomyocytes. The screens comprise the introduction of the candidate nucleic acids encoding candidate bioactive agents, followed by the application of arrythmogenic insults, with screening for bioactive agents that block specific depolarization of cell membrane. This may be detected using patch clamps, or via fluorescence techniques). Similarly, channel activity (for example, potassium and chloride channels) in cardiomyocytes could be regulated using the present methods in order to enhance contractibility and prevent or diminish arrythmia.

In a preferred embodiment, the present methods are used to screen for enhanced contractile properties of cardiomyocytes and diminish heart failure potential. The introduction of the libraries of the invention followed by measuring the rate of change of myosin polymerization/depolymerization using fluorescent techniques can be done. Bioactve agents which increase the rate of change of this phenomenon can result in a greater contractile response of the entire myocardium, similar to the effect seen with digitalis.

In a preferred embodiment, the present methods are useful to identify agents that will regulate the intracellular and sarcolemmal calcium cycling in cardiomyocytes in order to prevent arrhythmias. Bioactve agents are selected that regulate sodium-calcium exchange, sodium proton pump function, and regulation of calcium-ATPase activity.

In a preferred embodiment, the present methods are useful to identify agents that diminish embolic phenomena in arteries and arterioles leading to strokes (and other occlusive events leading to kidney failure and limb ischemia) and angina precipitating a myocardial infarct are selected. For example, bioactive agents which will diminish the adhesion of platelets and leukocytes, and thus diminish the occlusion events. Adhesion in this setting can be inhibited by the libraries of the invention being inserted into endothelial cells (quiescent cells, or activated by cytokines, i.e. IL-1, and growth factors, i.e. PDGF/EGF) and then screening for peptides that either: 1).downregulate adhesion molecule expression on the surface of the endothelial cells (binding assay); 2) block adhesion molecule activation on the surface of these cells (signaling assay); or 3) release in an autocrine manner peptides that block receptor binding to the cognate receptor on the adhering cell.

Embolic phenomena can also be addressed by activating proteolytic enzymes on the cell surfaces of endothelial cells, and thus releasing active enzyme which can digest blood clots. Thus, delivery of the libraries of the invention to endothelial cells is done, followed by standard fluorogenic assays, which will allow monitoring of proteolytic activity on the cell surface towards a known substrate. Bioactive agents can then be selected which activate specific enzymes towards specific substrates.

In a preferred embodiment, arterial inflammation in the setting of vasculitis and post-nfarction can be regulated by decreasing the chemotactic responses of leukocytes and mononuclear leukocytes. This can be accomplished by blocking chemotactic receptors and their responding pathways on these cells. Candidate bioactive libraries can be inserted into these cells, and the chemotactic response to diverse chemokines (for example, to the IL-8 family of chemokines, RANTES) inhibited in cell migration assays.

In a preferred embodiment, arterial restenosis following coronary angioplasty can be controlled by regulating the proliferation of vascular intimal cells and capillary and/or arterial endothelial cells. Candidate bioactive agent libraries can be inserted into these cell types and their proliferation in response to specific stimuli monitored. One application may be intracellular peptides which block the expression or function of c-myc and other oncogenes in smooth muscle cells to stop their proliferation. A second application may involve the expression of libraries in vascular smooth muscle cells to selectively induce their apoptosis. Application of small molecules derived from these peptides may require targeted drug delivery; this is available with stents, hydrogel coatings, and infusion-based catheter systems. Peptides which downregulate endothelin-1A receptors or which block the release of the potent vasoconstrictor and vascular smooth muscle cell mitogen endothelin-1 may also be candidates for therapeutics. Peptides can be isolated from these libraries which inhibit growth of these cells, or which prevent the adhesion of other cells in the circulation known to release autocrine growth factors, such as platelets (PDGF) and mononuclear leukocytes.

The control of capillary and blood vessel growth is an important goal in order to promote increased blood flow to ischemic areas (growth), or to cut-off the blood supply (angiogenesis inhibition) of tumors. Candidate bioactive agent libraries can be inserted into capillary endothelial cells and their growth monitored. Stimuli such as low oxygen tension and varying degrees of angiogenic factors can regulate the responses, and peptides isolated that produce the appropriate phenotype. Screening for antagonism of vascular endothelial cell growth factor, important in angiogenesis, would also be useful.

In a preferred embodiment, the present methods are useful in screening for decreases in atherosclerosis producing mechanisms to find peptides that regulate LDL and HDL metabolism. Candidate libraries can be inserted into the appropriate cells (including hepatocytes, mononuclear leukocytes, endothelial cells) and peptides selected which lead to a decreased release of LDL or diminished synthesis of LDL, or conversely to an increased release of HDL or enhanced synthesis of HDL. Bioactive agents can also be isolated from candidate libraries which decrease the production of oxidized LDL, which has been implicated in atherosclerosis and isolated from atherosclerotic lesions. This could occur by decreasing its expression, activating reducing systems or enzymes, or blocking the activity or production of enzymes implicated in production of oxidized LDL, such as 15-lipoxygenase in macrophages.

In a preferred embodiment, the present methods are used in screens to regulate obesity via the control of food intake mechanisms or diminishing the responses of receptor signaling pathways that regulate metabolism. Bioactive agents that regulate or inhibit the responses of neuropeptide Y (NPY), cholecystokinin and galanin receptors, are particularly desirable. Candidate libraries can be inserted into cells that have these receptors cloned into them, and inhibitory peptides selected that are secreted in an autocrine manner that block the signaling responses to galanin and NPY. In a similar manner, peptides can be found that regulate the leptin receptor.

In a preferred embodiment, the present methods are useful in neurobiology applications. Candidate libraries may be used for screening for anti-apoptotics for preservation of neuronal function and prevention of neuronal death. Initial screens would be done in cell culture. One application would include prevention of neuronal death, by apoptosis, in cerebral ischemia resulting from stroke. Apoptosis is known to be blocked by neuronal apoptosis inhibitory protein (NAIP); screens for its upregulation, or effecting any coupled step could yield peptides which selectively block neuronal apoptosis. Other applications include neurodegenerative diseases such as Alzheimer's disease and Huntington's disease.

In a preferred embodiment, the present methods are useful in bone biology applications. Osteoclasts are known to play a key role in bone remodeling by breaking down “old” bone, so that osteoblasts can lay down “new” bone. In osteoporosis one has an imbalance of this process. Osteoclast overactivity can be regulated by inserting candidate libraries into these cells, and then looking for bioactive agents that produce: 1) a diminished processing of collagen by these cells; 2) decreased pit formation on bone chips; and 3) decreased release of calcium from bone fragments.

The present methods may also be used to screen for agonists of bone morphogenic proteins, hormone mimetics to stimulate, regulate, or enhance new bone formation (in a manner similar to parathyroid hormone and calcitonin, for example). These have use in osteoporosis, for poorly healing fractures, and to accelerate the rate of healing of new fractures. Furthermore, cell lines of connective tissue origin can be treated with candidate libraries and screened for their growth, proliferation, collagen stimulating activity, and/or proline incorporating ability on the target osteoblasts. Alternatively, candidate libraries can be expressed directly in osteoblasts or chondrocytes and screened for increased production of collagen or bone.

In a preferred embodiment, the present methods are useful in skin biology applications. Keratinocyte responses to a variety of stimuli may result in: psoriasis, a proliferative change in these cells. Candidate libraries can be inserted into cells removed from active psoriatic plaques, and bioactve agents isolated which decrease the rate of growth of these cells.

In a preferred embodiment, the present methods are useful in the regulation or inhibition of keloid formation (i.e. excessive scarring). Candidate libraries inserted into skin connective tissue cells isolated from individuals with this condition, and bioactive agents isolated that decrease proliferation, collagen formation, or proline incorporation. Results from this work can be extended to treat the excessive scarring that also occurs in bum patients. If a common pepbde motif is found in the context of the keloid work, then it can be used widely in a topical manner to diminish scarring post burn.

Similarly, wound healing for diabetic ulcers and other chronic “failure to heal” conditions in the skin and extremities can be regulated by providing additional growth signals to cells which populate the skin and dermal layers. Growth factor mimetics may in fact be very useful for this condition. Candidate libraries can be inserted into skin connective tissue cells, and bioactive agents isolated which promote the growth of these cells under “harsh” conditions, such as low oxygen tension, low pH, and the presence of inflammatory mediators.

Cosmeceutcal applications of the present invention include the control of melanin production in skin melanocytes. A naturally occurring peptide, arbutin, is a tyrosine hydroxylase inhibitor, a key enzyme in the synthesis of melanin. Candidate libraries can be inserted into melanocytes and known stimuli that increase the synthesis of melanin applied to the cells. Bioactive agents can be isolated that inhibit the synthesis of melanin under these conditions.

In a preferred embodiment, the present methods are useful in endocrinology applications. The retroviral peptide library technology can be applied broadly to any endocrine, growth factor, cytokine or chemokine network which involves a signaling peptide or protein that acts in either an endocrine, paracrine or autocrine manner that binds or dimerizes a receptor and activates a signaling cascade that results in a known phenotypic or functional outcome. The methods are applied so as to isolate a peptde which either mimics the desired hormone (i.e., insulin, leptn, calcitonin, PDGF, EGF, EPO, GMCSF, IL-1-17, mimetics) or inhibits its action by either blocking the release of the hormone, blocking its binding to a specific receptor or carrier protein (for example, CRF binding protein), or inhibiting the intracellular responses of the specific target cells to that hormone. Selection of peptdes which increase the expression or release of hormones from the cells which normally produce them could have broad applications to conditions of hormonal deficiency.

In a preferred embodiment, the present methods are useful in infectious disease applications. Viral latency (herpes viruses such as CMV, EBV, HBV, and other viruses such as HIV) and their reactivation are a significant problem, particularly in immunosuppressed patents (patients with AIDS and transplant patients). The ability to block the reactivation and spread of these viruses is an important goal. Cell lines known to harbor or be susceptible to latent viral infection can be infected with the specific virus, and then stimuli applied to these cells which have been shown to lead to reactivation and viral replication. This can be followed by measuring viral titers in the medium and scoring cells for phenotypic changes. Candidate libraries can then be inserted into these cells under the above conditions, and peptdes isolated which block or diminish the growth and/or release of the virus. As with chemotherapeubcs, these experiments can also be done with drugs which are only partially effective towards this outcome, and bioactive agents isolated which enhance the virucidal effect of these drugs.

One example of many is the ability to block HIV-1 infection. HIV-1 requires CD4 and a co-receptor which can be one of several seven transmembrane G-protein coupled receptors. In the case of the infection of macrophages, CCR-5 is the required co-receptor, and there is strong evidence that a block on CCR-5 will result in resistance to HIV-1 infection. There are two lines of evidence for this statement. First, it is known that the natural ligands for CCR-5, the CC chemokines RANTES, MIP1a and MIP1 b are responsible for CD8+ mediated resistance to HIV. Second, individuals homozygous for a mutant allele of CCR-5 are completely resistant to HIV infection. Thus, an inhibitor of the CCR-5/HIV interaction would be of enormous interest to both biologists and clinicians. The extracellular anchored constructs offer superb tools for such a discovery. Into the transmembrane, epitope tagged, glycine-serine tethered constructs (ssTM V G20 E TM), one can place a cyclized peptide library of the general sequence CNNNNNNNNNNC or C-(X)_(n)-C. Then one infects a cell line that expresses CCR-5 with retroviruses containing this library. Using an antibody to CCR-5 one can use FACS to sort desired cells based on the binding of this antibody to the receptor. All cells which do not bind the antibody will be assumed contain inhibitors of this antibody binding site. These inhibitors, in the retroviral construct can be further assayed for their ability to inhibit HIV-1 entry.

Viruses are known to enter cells using specific receptors to bind to cells (for example, HIV uses CD4, coronavirus uses CD13, murine leukemia virus uses transport protein, and measles virus uses CD44) and to fuse with cells (HIV uses chemokine receptor). Candidate libraries can be inserted into target cells known to be permissive to these viruses, and bioactve agents isolated which block the ability of these viruses to bind and fuse with specific target cells.

In a preferred embodiment, the present invention finds use with infectious organisms. Intracellular organisms such as mycobacteria, listeria, salmonella, pneumocysts, yersinia,,leishmania, T. cruzi, can persist and replicate within cells, and become active in immunosuppressed patents. There are currently drugs on the market and in development which are either only partially effective or ineffective against these organisms. Candidate libraries can be inserted into specific cells infected with these organisms (pre- or post-infecton), and bioactve agents selected which promote the intracellular destruction of these organisms in a manner analogous to intracellular “antibiotic peptides” similar to magainins. In addition peptdes can be selected which enhance the cidal properties of drugs already under investigation which have insufficient potency by themselves, but when combined with a specific peptide from a candidate library, are dramatically more potent through a synergistic mechanism. Finally, bioactive agents can be isolated which alter the metabolism of these intracellular organisms, in such a way as to terminate their intracellular life cycle by inhibiting a key organismal event.

Antibiotic drugs that are widely used have certain dose dependent, tissue specific toxicities. For example renal toxicity is seen with the use of gentamicin, tobramycin, and amphotericin; hepatotoxicity is seen with the use of INH and rifampin; bone marrow toxicity is seen with chloramphenicol; and platelet toxicity is seen with ticarcillin, etc. These toxicites limit their use. Candidate libraries can be introduced into the specific cell types where specific changes leading to cellular damage or apoptosis by the antibiotics are produced, and bioactive agents can be isolated that confer protection, when these cells are treated with these specific antibiotics.

Furthermore, the present invention finds use in screening for bioactve agents that block antibiotic transport mechanisms. The rapid secretion from the blood stream of certain antibiotics limits their usefulness. For example penicillins are rapidly secreted by certain transport mechanisms in the kidney and choroid plexus in the brain. Probenecid is known to block this transport and increase serum and tissue levels. Candidate agents can be inserted into specific cells derived from kidney cells and cells of the choroid plexus known to have active transport mechanisms for antbiotics. Bioactve agents can then be isolated which block the active transport of specific antibiotics and thus extend the serum halflife of these drugs.

In a preferred embodiment, the present methods are useful in drug toxicities and drug resistance applications. Drug toxicity is a significant clinical problem. This may manifest itself as specific tissue or cell damage with the result that the drug's effectiveness is limited. Examples include myeloablaton in high dose cancer chemotherapy, damage to epithelial cells lining the airway and gut, and hair loss. Specific examples include adriamycin induced cardiomyocyte death, cisplatininanduced kidney toxicity, vincristne-induced gut motility disorders, and cyclosporin-induced kidney damage. Candidate libraries can be introduced into specific cell types with characteristic drug-induced phenotypic or functional responses, in the presence of the drugs, and agents isolated which reverse or protect the specific cell type against the toxic changes when-exposed to the drug. These effects may manifest as blocking the drug induced apoptosis of the cell of interest, thus initial screens will be for survival of the cells in the presence of high levels of drugs or combinations of drugs used in combination chemotherapy.

Drug toxicity may be due to a specific metabolite produced in the liver or kidney which is highly toxic to specific cells, or due to drug interactions in the liver which block or enhance the metabolism of an administered drug. Candidate libraries can be introduced into liver or kidney cells following the exposure of these cells to the drug known to produce the toxic metabolite. Bioactive agents can be isolated which alter how the liver or kidney cells metabolize the drug, and specific agents identified which prevent the generation of a specific toxic metabolite. The generation of the metabolite can be followed by mass spectrometry, and phenotypic changes can be assessed by microscopy. Such a screen can also be done in cultured hepatocytes, cocultured with readout cells which are specifically sensitive to the toxic metabolite. Applications include reversible (to limit toxicity) inhibitors of enzymes involved in drug metabolism.

Multiple drug resistance, and hence tumor cell selection, outgrowth, and relapse, leads to morbidity and mortality in cancer patients. Candidate libraries can be introduced into tumor cell lines (primary and cultured) that have demonstrated specific or multiple drug resistance. Bioactive agents can then be identified which confer drug sensitivity when the cells are exposed to the drug of interest, or to drugs used in combination chemotherapy. The readout can be the onset of apoptosis in these cells, membrane permeability changes, the release of intracellular ions and fluorescent markers. The cells in which multidrug resistance involves membrane transporters can be preloaded with fluorescent transporter substrates, and selection carried out for peptides which block the normal efflux of fluorescent drug from these cells. Candidate libraries are particularly suited to screening for peptides which reverse poorly characterized or recently discovered intracellular mechanisms of resistance or mechanisms for which few or no chemosensitizers currently exist, such as mechanisms involving LRP (lung resistance protein). This protein has been implicated in multidrug resistance in ovarian carcinoma, metastatic malignant melanoma, and acute myeloid leukemia. Particularly interesting examples include screening for agents which reverse more than one important resistance mechanism in a single cell, which occurs in a subset of the most drug resistant cells, which are also important targets. Applications would include screening for peptide inhibitors of both MRP (multidrug resistance related protein) and LRP for treatment of resistant cells in metastatic melanoma, for inhibitors of both p-glycoprotein and LRP in acute myeloid leukemia and for inhibition (by any mechanism) of all three proteins for treating pan-resistant cells.

In a preferred embodiment, the present methods are useful in improving the performance of existing or developmental drugs. First pass metabolism of orally administered drugs limits their oral bioavailability, and can result in diminished efficacy as well as the need to administer more drug for a desired effect. Reversible inhibitors of enzymes involved in first pass metabolism may thus be a useful adjunct enhancing the efficacy of these drugs. First pass metabolism occurs in the liver, thus inhibitors of the corresponding catabolic enzymes may. enhance the effect of the cognate drugs. Reversible inhibitors would be delivered at the same time as, or slightly before, the drug of interest. Screening of candidate libraries in hepatocytes for inhibitors (by any mechanism, such as protein downregulation as well as a direct inhibition of activity) of particularly problematical isozymes would be of interest. These include the CYP3A4 isozymes of cytochrome P450, which are involved in the first pass metabolism of the anti-HIV drugs saquinavir and indinavir. Other applications could include reversible inhibitors of UDP-glucuronyltransferases, sulfotransferases, N-acetyltransferases, epoxide hydrolases, and glutathione S-transferases, depending on the drug. Screens would be done in cultured hepatocytes or liver microsomes, and could involve antibodies recognizing the specific modification performed in the liver, or cocultured readout cells, if the metabolite had a different bioactivity than the untransformed drug. The enzymes modifying the drug would not necessarily have to be known, if screening was for lack of alteration of the drug.

In a preferred embodiment, the present methods are useful in immunobiology, inflammation, and allergic response applications. Selective regulation of T lymphocyte responses is a desired goal in order to modulate immune-mediated diseases in a specific manner. Candidate libraries can be introduced into specific T cell subsets (TH1, TH2, CD4+, CD8+, and others) and the responses which characterize those subsets (cytokine generation, cytotoxicity, proliferation in response to antigen being presented by a mononuclear leukocyte, and others) modified by members of the library. Agents can be selected which increase or diminish the known T cell subset physiologic response. This approach will be useful in any number of conditions, including: 1) autoimmune diseases where one wants to induce a tolerant state (select a peptide that inhibits T cell subset from recognizing a self-antigen bearing cell); 2) allergic diseases where one wants to decrease the stimulation of IgE producing cells (select peptide which blocks release from T cell subsets of specific B-cell stimulating cytokines which induce switch to IgE production); 3) in transplant: patients where one wants to induce selective immunosuppression (select peptide that diminishes proliferative responses of host T cells to foreign antigens); 4) in lymphoproliferative states-where one wants to inhibit the growth or sensitize a specific T cell tumor to chemotherapy and/or radiation; 5) in tumor surveillance where one wants to inhibit the killing of cytotoxic T cells by Fas ligand bearing tumor cells; and 5) in T cell mediated inflammatory diseases such as Rheumatoid arthritis, Connective tissue diseases (SLE), Multiple sclerosis, and inflammatory bowel disease, where onewants too inhibit the proliferation of disease-causing T cells (promote their selective apoptosis) and the resulting selective destruction of target tissues (cartilage, connective tissue, oligodendrocytes, gut endothelial cells, respectively).

Regulation of B cell responses will permit a more selective modulation of the type and amount of immunoglobulin made and secreted by specific B cell subsets. Candidate libraries can be inserted into B cells and bioactive agents selected which inhibit the release and synthesis of a specific immunoglobulin. This may be useful in autoimmune diseases characterized by the overproduction of auto antibodies and the production of allergy causing antibodies, such as IgE. Agents can also be identified which inhibit or enhance the binding of a specific immunoglobulin subclass to a specific antigen either foreign of self. Finally, agents can be selected which inhibit the binding of a specific immunoglobulin subclass to its receptor on specific cell types.

Similarly, agents which affect cytokine production may be selected, generally using two cell systems. For example, cytokine production from macrophages, monocytes, etc. may be evaluated. Similarly, agents which mimic cytokines, for example erythropoetin and IL1-17, may be selected, or agents that bind cytokines such as TNF-α, before they bind:their receptor.

Antigen processing by mononuclear leukocytes (ML) is an important early step in the immune system's ability to recognize and eliminate foreign proteins. Candidate agents can be inserted into ML cell lines and agents selected which alter the intracellular processing of foreign peptides and sequence of the foreign peptide that is presented to T cells by MLs on their cell surface in the context of Class II MHC. One can look for members of the library that enhance immune responses of a particular T cell subset (for example, the peptide would in fact work as a vaccine), or look for a library member that binds more tightly to MHC, thus displacing naturally occurring pepbdes, but nonetheless the agent would be less immunogenic (less stimulatory to a specific T cell clone). This agent would in fact induce immune tolerance and/or diminish immune responses to foreign proteins. This approach could be used in transplantation, autoimmune diseases, and allergic diseases.

The release of inflammatory mediators (cytokines, leukotrienes, prostaglandins, platelet activating factor, histamine; neuropeptides, and other peptide and lipid mediators) is a key element in maintaining and amplifying aberrant immune responses. Candidate libraries can be inserted into MLs, mast cells, eosinophils, and other cells participating in a specific inflammatory response, and bioactive agents selected which inhibit the synthesis, release and binding to the cognate receptor of each of these types of mediators.

In a preferred embodiment, the present methods are useful in biotechnology applications. Candidate library expression in mammalian cells can also be considered for other pharmaceutical-related applications, such as modification of protein expression, protein folding, or protein secretion. One such example would be in commercial production of protein pharmaceuticals in CHO or other cells. Candidate libraries resulting in bioactive agents which select for an increased cell growth rate (perhaps peptides mimicking growth factors or acting as agonists of growth factor signal transduction pathways), for pathogen resistance (see previous section), for lack of sialylation or glycosylation (by blocking glycotransferases or rerouting trafficking of the protein in the cell), for allowing growth on autoclaved media, or for growth in serum free media, would all increase productivity and decrease costs in the production of protein pharmaceuticals.

Peptides displayed on the surface of circulating cells can be used as tools to identify. organ, tissue, and cell specific peptide targeting sequences. Any cell introduced into the bloodstream of an animal expressing a library targeted to the cell surface can be selected for specific organ and tissue targeting. The bioactive agent sequence identified can then be coupled to an antibody, enzyme, drug, imaging agent or substance for which organ targeting is desired.

Other agents which may be selected using the present invention include: 1) agents which block the activity of transcription factors, using cell lines with reporter genes; 2) agents which block the interaction of two known proteins in cells, using the absence of normal cellular functions, the mammalian two hybrid system or fluorescence resonance energy transfer mechanisms for detection; and 3) agents may be identified by tethering a candidate peptide to a protein binding region to allow interactions with molecules sterically close, i.e. within a signalling pathway, to localize the effects to a functional area of interest.

All references cited herein are incorporated by reference in their entirety. 

1-20. (canceled)
 21. A bi-directionally cloned cDNA expression vector library comprising: a) a first plurality of expression vectors, each comprising: i. a promoter that is active in a mammalian cell; and ii. a cDNA fragment that is operably linked to said promoter in a sense orientation; and b) a second plurality of expression vectors, each comprising: i. said promoter; and ii. a cDNA fragment that is operably linked to said promoter in an antisense orientation.
 22. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said expression vectors are retroviral expression vectors.
 23. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said expression vectors comprises cDNA fragments from a mammalian source.
 24. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said expression vectors further comprise a coding sequence for a reporter protein, operably linked to said promoter.
 25. The bi-directionally cloned cDNA expression vector library of claim 21, wherein, wherein said reporter protein is a green fluorescent protein (GFP).
 26. The bi-directionally cloned cDNA expression vector library of claim 24, wherein said coding sequence and said cDNA fragment are separated by an internal ribosomal entry site (IRES).
 27. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said promoter is a constitutive promoter.
 28. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said promoter is an inducible promoter.
 29. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said library comprises from 10³ to 10⁹ vectors.
 30. The bi-directionally cloned cDNA expression vector library of claim 21, wherein said library is made by a method comprising: contacting mRNA molecules with a primer under conditions to produce a double-stranded cDNA, said primer having a site for a first restriction endonuclease; cleaving said double stranded cDNA to produce cDNA fragments; ligating a double-stranded adaptor to each end of said cDNA fragments to produce adaptor-modified cDNAs, said double stranded adaptor comprising a site for a second restriction endonuclease; contacting said adaptor-modified cDNAs with said first restriction endonuclease and said second restriction endonuclease to produce digested cDNAs; and, ligating said digested cDNAs into vectors to produce a library of vectors; to make said library.
 31. A population of cells comprising the bi-directionally cloned cDNA expression vector library of claim
 21. 32. The population of cells of claim 21, wherein said cells are mammalian cells. 